Louis BECQUEY / RNANet

Go to a project
Toggle navigation Toggle navigation pinning
Aglaé TABOT
ad0e234c 2 parents 9dedcd5b 60f0af5a

Merge branch 'master' into stage_aglae

Inline Side-by-side
Showing 18 changed files with 1027 additions and 1606 deletions
......@@ -23,3 +23,5 @@ scripts/*.sh
scripts/*.tar
scripts/measure.py
scripts/recompute_some_chains.py
scripts/convert_rna_jsons.py
scripts/recompute_family.py
......
############################################################################################
v 1.6 beta, August 2021
Aglaé Tabot joins the development team. Khodor Hannoush leaves.
FEATURE CHANGES
- Distinct options --cmalign-opts and --cmalign-rrna-opts allow to adapt the parameters for LSU and SSU families.
The LSU and SSU are now aligned with Infernal options '--cpu 10 --mxsize 8192 --mxtau 0.1', which is slow,
requires up to 100 GB of RAM, and yields a suboptimal alignment (tau=0.1 is quite bad), but is homogenous with the other families.
- The LSU and SSU therefore have defined cm_coords fields, and therefore distance matrices can be computed.
- Distances matrices are computed on all availables molecules of the family by default, but you can use statistics.py --non-redundant to only
select the equivalence class representatives at a given resolution into account (new option). For storage reasons, rRNAs are always run in
this mode (but this might change in the future : space required is 'only' ~300 GB).
- We now provide for download the renumbered (standardised) 3D MMCIF files, the nucleotides being numbered by their "index_chain" in the database.
- We now provide for download the sequences of the 3D chains aligned by Rfam family (without Rfam sequences, which have been removed).
- statistics.py now computes histograms and a density estimation with Gaussian mixture models for a large set of geometric parameters,
measured on the unmapped data at a given resolution threshold. The parameters include:
* All atom bonded distances and torsion angles
* Distances, flat angles and torsion angles in the Pyle/VFold model
* Distances, flat angles and torsion anfles in the HiRE-RNA model
* Sequence-dependant geometric parameters of the basepairs for all non-canonical basepairs in the HiRE-RNA model.
The data is saved as JSON files of parameters, and numerous figures are produced to illustrate the distributions.
The number of gaussians to use in the GMMs are hard-coded in geometric_stats.py after our first estimation. If you do not want to trust this estimation,
you can ignore it with option --rescan-nmodes. An exploration of the number of Gaussians from 1 to 8 will be performed, and the best GMM will be kept.
BUG CORRECTIONS
- New code file geometric_stats.py
- New automation script that starts from scratch
- Many small fixes, leading to the support of many previously "known issues"
- Performance tweaks
TECHNICAL CHANGES
- Switched to DSSR Pro.
- Switched to esl-alimerge instead of cmalign --merge to merge alignments.
- Tested successfully with Python 3.9.6 + BioPython 1.79.
However, the production server still runs with Python 3.8.1 + BioPython 1.78.
############################################################################################
v 1.5 beta, April 2021
FEATURE CHANGES
......
MIT License
Copyright (c) 2019 Louis Becquey
Copyright (c) 2019-2021 IBISC, Université Paris Saclay
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
......
......@@ -10,6 +10,7 @@ Contents:
* [Database tables documentation](doc/Database.md)
* [FAQ](doc/FAQ.md)
* [Troubleshooting](#troubleshooting)
* [Known Issues and Feature Requests](doc/KnownIssues.md)
* [Contact](#contact)
## Cite us
......@@ -18,15 +19,13 @@ Contents:
Additional relevant references:
The "ProteinNet" philosophy which inspired this work:
* AlQuraishi, M. (2019b). **ProteinNet: A standardized data set for machine learning of protein structure.** *BMC Bioinformatics*, 20(1), 311
If you use our annotations by DSSR, you might want to cite:
* Lu, X.-J.et al.(2015). **DSSR: An integrated software tool for dissecting the spatial structure of RNA.** *Nucleic Acids Research*, 43(21), e142–e142.
If you use our multiple sequence alignments and homology data, you might want to cite:
* Pruesse, E. et al.(2012). **Sina: accurate high-throughput multiple sequence alignment of ribosomal RNA genes.** *Bioinformatics*, 28(14), 1823–1829
* Nawrocki, E. P. and Eddy, S. R. (2013). **Infernal 1.1: 100-fold faster RNA homology searches.** *Bioinformatics*, 29(22), 2933–2935.
* Pruesse, E. et al.(2012). **Sina: accurate high-throughput multiple sequence alignment of ribosomal RNA genes.** *Bioinformatics*, 28(14), 1823–1829
# What is RNANet ?
......@@ -39,7 +38,8 @@ Most interestingly, nucleotides have been renumered in a standardized way, and t
## Methodology
We use the Rfam mappings between 3D structures and known Rfam families, using the sequences that are known to belong to an Rfam family (hits provided in RF0XXXX.fasta files from Rfam).
Future versions might compute a real MSA-based clusering directly with Rfamseq ncRNA sequences, like ProteinNet does with protein sequences, but this requires a tool similar to jackHMMER in the Infernal software suite, which is not available yet.
Future versions might compute a real MSA-based clusering directly with Rfamseq ncRNA sequences, like ProteinNet does with protein sequences, but this requires a tool similar to jackHMMER in the Infernal software suite, which is not available yet.
If interested by such approaches, the user may check tools like RNAlien.
This script prepares the dataset from available public data in PDB, RNA 3D Hub, Rfam and SILVA.
......@@ -48,15 +48,16 @@ This script prepares the dataset from available public data in PDB, RNA 3D Hub,
The script follows these steps:
To gather structures:
* Gets a list of 3D structures containing RNA from BGSU's non-redundant list (but keeps the redundant structures /!\\),
* Gets a list of 3D structures containing RNA from BGSU's non-redundant list (redundancy can be kept or eliminated, see command line option `--redundant`),
* Asks Rfam for mappings of these structures onto Rfam families (~50% of structures have a direct mapping, some more are inferred using the redundancy list)
* Downloads the corresponding 3D structures (mmCIFs)
* If desired, extracts the right chain portions that map onto an Rfam family to a separate mmCIF file
* Standardizes the residue numbering from 1 to N, including missing residues (gaps)
* If desired, extracts the renumbered chain portions that map onto an Rfam family to a separate mmCIF file
To compute homology information:
* Extract the sequence for every 3D chain
* Extracts the sequence of every 3D chain
* Downloads Rfamseq ncRNA sequence hits for the concerned Rfam families (or ARB databases of SSU or LSU sequences from SILVA for rRNAs)
* Realigns Rfamseq hits and sequences from the 3D structures together to obtain a multiple sequence alignment for each Rfam family (using `cmalign --cyk`, except for ribosomal LSU and SSU, where SINA is used)
* Realigns Rfamseq hits and sequences from the 3D structures together to obtain a multiple sequence alignment for each Rfam family (using `cmalign`, but SINA can be used for ribosomal LSU and SSU)
* Computes nucleotide frequencies at every position for each alignment
* Map each nucleotide of a 3D chain to its position in the corresponding family sequence alignment
......@@ -65,6 +66,15 @@ To compute 3D annotations:
Finally, export this data from the SQLite database into flat CSV files.
Statistical analysis of the structures:
* Computes statistics about the amount of data from various resolutions and experimental methods (by RNA family)
* Computes basic statistics about the frequency of (modified) nucleotides by chain and by family,
* Computes basic statistics about the frequencies of non-canonical interactions,
* Computes density estimations (using Gaussian mixtures) for various geometrical parameters like distances and torsion angles for different representations : all-atom, the Pyle/VFold model, and the HiRE-RNA model,
* Computes pairwise residue distance matrices for each chain, and average + std-dev by RNA family
* Computes sequence identity matrices for each RNA family (based on the alignments)
* Saves covariance models (Infernal .cm files) for each RNA family
## Data provided
We provide couple of resources to exploit this dataset. You can download them on [EvryRNA](https://evryrna.ibisc.univ-evry.fr/evryrna/rnanet/rnanet_home).
......
......@@ -31,7 +31,7 @@ import time
import traceback
import warnings
from functools import partial, wraps
from multiprocessing import Pool, Manager
from multiprocessing import Pool, Manager, Value
from time import sleep
from tqdm import tqdm
from setproctitle import setproctitle
......@@ -45,42 +45,44 @@ from Bio.PDB.PDBIO import Select
runDir = os.getcwd()
def trace_unhandled_exceptions(func):
"""
Captures exceptions even in parallel sections of the code and child processes,
and throws logs in red to stderr and to errors.txt.
Should be defined before the classes that use it.
"""
@wraps(func)
def wrapped_func(*args, **kwargs):
try:
return func(*args, **kwargs)
except:
s = traceback.format_exc()
with open(runDir + "/errors.txt", "a") as f:
f.write("Exception in "+func.__name__+"\n")
f.write(s)
f.write("\n\n")
warn('Exception in '+func.__name__, error=True)
print(s)
if not "KeyboardInterrupt" in s:
with open(runDir + "/errors.txt", "a") as f:
f.write("Exception in "+func.__name__+"\n")
f.write(s)
f.write("\n\n")
warn('Exception in '+func.__name__, error=True)
print(s)
return wrapped_func
pd.set_option('display.max_rows', None)
sqlite3.enable_callback_tracebacks(True)
sqlite3.register_adapter(np.int64, lambda val: int(val)) # Tell Sqlite what to do with <class numpy.int64> objects ---> convert to int
sqlite3.register_adapter(np.float64, lambda val: float(val)) # Tell Sqlite what to do with <class numpy.float64> objects ---> convert to float
m = Manager()
running_stats = m.list()
running_stats.append(0) # n_launched
running_stats.append(0) # n_finished
running_stats.append(0) # n_skipped
n_launched = Value('i', 0)
n_finished = Value('i', 0)
n_skipped = Value('i', 0)
path_to_3D_data = "tobedefinedbyoptions"
path_to_seq_data = "tobedefinedbyoptions"
python_executable = "python"+".".join(platform.python_version().split('.')[:2]) # Cuts python3.8.1 into python3.8 for example.
validsymb = '\U00002705'
warnsymb = '\U000026A0'
errsymb = '\U0000274C'
LSU_set = {"RF00002", "RF02540", "RF02541",
"RF02543", "RF02546"} # From Rfam CLAN 00112
SSU_set = {"RF00177", "RF02542", "RF02545",
"RF01959", "RF01960"} # From Rfam CLAN 00111
LSU_set = {"RF00002", "RF02540", "RF02541", "RF02543", "RF02546"} # From Rfam CLAN 00112
SSU_set = {"RF00177", "RF02542", "RF02545", "RF01959", "RF01960"} # From Rfam CLAN 00111
no_nts_set = set()
weird_mappings = set()
......@@ -103,17 +105,15 @@ class MutableFastaIterator(FastaIterator):
first_word = title.split(None, 1)[0]
except IndexError:
assert not title, repr(title)
# Should we use SeqRecord default for no ID?
first_word = ""
yield SeqRecord(
MutableSeq(sequence), id=first_word, name=first_word, description=title,
)
yield SeqRecord(MutableSeq(sequence), id=first_word, name=first_word, description=title)
class SelectivePortionSelector(object):
"""Class passed to MMCIFIO to select some chain portions in an MMCIF file.
Validates every chain, residue, nucleotide, to say if it is in the selection or not.
The primary use is to select the portion of a chain which is mapped to a family.
"""
def __init__(self, model_id, chain_id, valid_resnums, khetatm):
......@@ -156,123 +156,6 @@ class SelectivePortionSelector(object):
return 1
_select=Select()
def save_mmcif(ioobj, out_file, select=_select, preserve_atom_numbering=False):
# reuse and modification of the source code of Biopython
# to have the 2 columns of numbering of residues numbered with the index_chain of DSSR
if isinstance(out_file, str):
fp = open(out_file, "w")
close_file = True
else:
fp = out_file
close_file = False
atom_dict = defaultdict(list)
for model in ioobj.structure.get_list():
if not select.accept_model(model):
continue
# mmCIF files with a single model have it specified as model 1
if model.serial_num == 0:
model_n = "1"
else:
model_n = str(model.serial_num)
# This is used to write label_entity_id and label_asym_id and
# increments from 1, changing with each molecule
entity_id = 0
if not preserve_atom_numbering:
atom_number = 1
for chain in model.get_list():
if not select.accept_chain(chain):
continue
chain_id = chain.get_id()
if chain_id == " ":
chain_id = "."
# This is used to write label_seq_id,
# remaining blank for hetero residues
prev_residue_type = ""
prev_resname = ""
for residue in chain.get_unpacked_list():
if not select.accept_residue(residue):
continue
hetfield, resseq, icode = residue.get_id()
if hetfield == " ":
residue_type = "ATOM"
label_seq_id = str(resseq)
else:
residue_type = "HETATM"
label_seq_id = "."
resseq = str(resseq)
if icode == " ":
icode = "?"
resname = residue.get_resname()
# Check if the molecule changes within the chain
# This will always increment for the first residue in a
# chain due to the starting values above
if residue_type != prev_residue_type or (
residue_type == "HETATM" and resname != prev_resname
):
entity_id += 1
prev_residue_type = residue_type
prev_resname = resname
label_asym_id = ioobj._get_label_asym_id(entity_id)
for atom in residue.get_unpacked_list():
if select.accept_atom(atom):
atom_dict["_atom_site.group_PDB"].append(residue_type)
if preserve_atom_numbering:
atom_number = atom.get_serial_number()
atom_dict["_atom_site.id"].append(str(atom_number))
if not preserve_atom_numbering:
atom_number += 1
element = atom.element.strip()
if element == "":
element = "?"
atom_dict["_atom_site.type_symbol"].append(element)
atom_dict["_atom_site.label_atom_id"].append(
atom.get_name().strip()
)
altloc = atom.get_altloc()
if altloc == " ":
altloc = "."
atom_dict["_atom_site.label_alt_id"].append(altloc)
atom_dict["_atom_site.label_comp_id"].append(
resname.strip()
)
atom_dict["_atom_site.label_asym_id"].append(label_asym_id)
# The entity ID should be the same for similar chains
# However this is non-trivial to calculate so we write "?"
atom_dict["_atom_site.label_entity_id"].append("?")
atom_dict["_atom_site.label_seq_id"].append(label_seq_id)
atom_dict["_atom_site.pdbx_PDB_ins_code"].append(icode)
coord = atom.get_coord()
atom_dict["_atom_site.Cartn_x"].append("%.3f" % coord[0])
atom_dict["_atom_site.Cartn_y"].append("%.3f" % coord[1])
atom_dict["_atom_site.Cartn_z"].append("%.3f" % coord[2])
atom_dict["_atom_site.occupancy"].append(
str(atom.get_occupancy())
)
atom_dict["_atom_site.B_iso_or_equiv"].append(
str(atom.get_bfactor())
)
atom_dict["_atom_site.auth_seq_id"].append(resseq)
atom_dict["_atom_site.auth_asym_id"].append(chain_id)
atom_dict["_atom_site.pdbx_PDB_model_num"].append(model_n)
# Data block name is the structure ID with special characters removed
structure_id = ioobj.structure.id
for c in ["#", "$", "'", '"', "[", "]", " ", "\t", "\n"]:
structure_id = structure_id.replace(c, "")
atom_dict["data_"] = structure_id
# Set the dictionary and write out using the generic dictionary method
ioobj.dic = atom_dict
ioobj._save_dict(fp)
if close_file:
fp.close()
class Chain:
"""
The object which stores all our data and the methods to process it.
......@@ -379,7 +262,7 @@ class Chain:
new_s.add(new_model)
# renumber this structure (portion of the original) with the index_chain and save it in a cif file
t=pdb.Structure.Structure(new_s.get_id())
t = pdb.Structure.Structure(new_s.get_id())
for model in new_s:
new_model_t=pdb.Model.Model(model.get_id())
for chain in model:
......@@ -406,7 +289,7 @@ class Chain:
# particular case 6n5s_1_A, residue 201 in the original cif file (resname = G and HETATM = H_G)
if nt == 'A' or (nt == 'G' and (self.chain_label != '6n5s_1_A' or resseq != 201)) or nt == 'C' or nt == 'U' or nt in ['DG', 'DU', 'DC', 'DA', 'DI', 'DT' ] or nt == 'N' or nt == 'I' :
res=chain[(' ', resseq, icode_res)]
else : #modified nucleotides (e.g. chain 5l4o_1_A)
else : # modified nucleotides (e.g. chain 5l4o_1_A)
het='H_' + nt
res=chain[(het, resseq, icode_res)]
res_id=res.get_id()
......@@ -424,13 +307,11 @@ class Chain:
for atom in list(res.get_atoms()):
# rename the remaining phosphate group to P, OP1, OP2, OP3
if atom.get_name() in ['PA', 'O1A', 'O2A', 'O3A'] and res_name != 'RIA':
# RIA is a residue made up of 2 riboses and 2 phosphates,
# so it has an O2A atom between the C2A and C1 'atoms,
# and it also has an OP2 atom attached to one of its phosphates
# (see chains 6fyx_1_1, 6zu9_1_1, 6fyy_1_1, 6gsm_1_1 , 3jaq_1_1 and 1yfg_1_A)
# we do not modify the atom names of RIA residue
# RIA is a residue made up of 2 riboses and 2 phosphates,
# so it has an O2A atom between the C2A and C1 'atoms,
# and it also has an OP2 atom attached to one of its phosphates
# (see chains 6fyx_1_1, 6zu9_1_1, 6fyy_1_1, 6gsm_1_1 , 3jaq_1_1 and 1yfg_1_A)
# we do not modify the atom names of RIA residue
if atom.get_name() == 'PA':
atom_name = 'P'
if atom.get_name() == 'O1A':
......@@ -440,7 +321,7 @@ class Chain:
if atom.get_name() == 'O3A':
atom_name = 'OP3'
new_atom_t = pdb.Atom.Atom(atom_name, atom.get_coord(), atom.get_bfactor(), atom.get_occupancy(), atom.get_altloc(), atom_name, atom.get_serial_number())
else :
else:
new_atom_t=atom.copy()
new_residu_t.add(new_atom_t)
new_chain_t.add(new_residu_t)
......@@ -750,12 +631,24 @@ class Chain:
if nt2 in res_ids:
interacts[nt2_idx] += 1
if paired[nt2_idx] == "":
pair_type_LW[nt2_idx] = lw_pair[0] + lw_pair[2] + lw_pair[1]
pair_type_DSSR[nt2_idx] = dssr_pair[0] + dssr_pair[3] + dssr_pair[2] + dssr_pair[1]
if lw_pair != "--":
pair_type_LW[nt2_idx] = lw_pair[0] + lw_pair[2] + lw_pair[1]
else:
pair_type_LW[nt2_idx] = "--"
if dssr_pair != "--":
pair_type_DSSR[nt2_idx] = dssr_pair[0] + dssr_pair[3] + dssr_pair[2] + dssr_pair[1]
else:
pair_type_DSSR[nt2_idx] = "--"
paired[nt2_idx] = str(nt1_idx + 1)
else:
pair_type_LW[nt2_idx] += ',' + lw_pair[0] + lw_pair[2] + lw_pair[1]
pair_type_DSSR[nt2_idx] += ',' + dssr_pair[0] + dssr_pair[3] + dssr_pair[2] + dssr_pair[1]
if lw_pair != "--":
pair_type_LW[nt2_idx] += ',' + lw_pair[0] + lw_pair[2] + lw_pair[1]
else:
pair_type_LW[nt2_idx] += ",--"
if dssr_pair != "--":
pair_type_DSSR[nt2_idx] += ',' + dssr_pair[0] + dssr_pair[3] + dssr_pair[2] + dssr_pair[1]
else:
pair_type_DSSR[nt2_idx] += ",--"
paired[nt2_idx] += ',' + str(nt1_idx + 1)
# transform nt_id to shorter values
......@@ -787,7 +680,8 @@ class Chain:
return df
def register_chain(self, df):
"""Saves the extracted 3D data to the database.
"""
Saves the extracted 3D data to the database.
"""
setproctitle(f"RNANet.py {self.chain_label} register_chain()")
......@@ -920,6 +814,10 @@ class Monitor:
class Downloader:
"""
An object with methods to download public data from the internet.
"""
def download_Rfam_PDB_mappings(self):
"""Query the Rfam public MySQL database for mappings between their RNA families and PDB structures.
......@@ -1170,6 +1068,10 @@ class Mapping:
class Pipeline:
"""
The RNANet pipeline steps.
"""
def __init__(self):
self.dl = Downloader()
self.known_issues = [] # list of chain_labels to ignore
......@@ -1189,6 +1091,7 @@ class Pipeline:
self.REUSE_ALL = False
self.REDUNDANT = False
self.ALIGNOPTS = None
self.RRNAALIGNOPTS = ["--mxsize", "8192", "--cpu", "10", "--maxtau", "0.1"]
self.STATSOPTS = None
self.USESINA = False
self.SELECT_ONLY = None
......@@ -1207,7 +1110,7 @@ class Pipeline:
try:
opts, _ = getopt.getopt(sys.argv[1:], "r:fhs", ["help", "resolution=", "3d-folder=", "seq-folder=", "keep-hetatm=",
"only=", "cmalign-opts=", "stats-opts=", "maxcores=", "sina", "from-scratch",
"only=", "cmalign-opts=", "cmalign-rrna-opts=", "stats-opts=", "maxcores=", "sina", "from-scratch",
"full-inference", "no-homology", "redundant", "ignore-issues", "extract",
"all", "no-logs", "archive", "update-homologous", "version"])
except getopt.GetoptError as err:
......@@ -1256,6 +1159,7 @@ class Pipeline:
"\n\t\t\t\t need of RAM. Should be a number between 1 and your number of CPUs. Note that portions"
"\n\t\t\t\t of the pipeline already limit themselves to 50% or 70% of that number by default.")
print("--cmalign-opts=…\t\tA string of additional options to pass to cmalign aligner, e.g. \"--nonbanded --mxsize 2048\"")
print("--cmalign-rrna-opts=…\tLike cmalign-opts, but applied for rRNA (large families, memory-heavy jobs).")
print("--archive\t\t\tCreate tar.gz archives of the datapoints text files and the alignments,"
"\n\t\t\t\t and update the link to the latest archive. ")
print("--no-logs\t\t\tDo not save per-chain logs of the numbering modifications.")
......@@ -1321,10 +1225,12 @@ class Pipeline:
path_to_seq_data + "realigned",
path_to_seq_data + "rfam_sequences"])
self.REUSE_ALL = True
elif opt == "cmalign-opts":
self.ALIGNOPTS = arg
elif opt == "stats-opts":
self.STATSOPTS = " ".split(arg)
elif opt == "--cmalign-opts":
self.ALIGNOPTS = arg.split(" ")
elif opt == "--cmalign-rrna-opts":
self.RRNAALIGNOPTS = arg.split(" ")
elif opt == "--stats-opts":
self.STATSOPTS = arg.split(" ")
elif opt == "--all":
self.REUSE_ALL = True
self.USE_KNOWN_ISSUES = False
......@@ -1382,7 +1288,7 @@ class Pipeline:
# If self.FULLINFERENCE is False, the extended list is already filtered to remove
# the chains which already are in the database.
print("> Building list of structures...", flush=True)
p = Pool(initializer=init_worker, initargs=(tqdm.get_lock(),), processes=ncores)
p = Pool(initializer=init_with_tqdm, initargs=(tqdm.get_lock(),), processes=ncores)
try:
pbar = tqdm(full_structures_list, maxinterval=1.0, miniters=1,
......@@ -1421,6 +1327,7 @@ class Pipeline:
conn.execute('pragma journal_mode=wal')
for eq_class, representative, codelist in tqdm(full_structures_list, desc="Eq. classes"):
codes = codelist.replace('+', ',').split(',')
representatives = representative.replace('+', ',').split(',')
# Simply convert the list of codes to Chain() objects
if self.REDUNDANT:
......@@ -1438,18 +1345,19 @@ class Pipeline:
if not len(res) or self.REUSE_ALL: # the chain is NOT yet in the database, or this is a known issue
self.update.append(Chain(pdb_id, pdb_model, pdb_chain_id, chain_label, eq_class))
else:
nr = representative.split('|')
pdb_id = nr[0].lower()
pdb_model = int(nr[1])
pdb_chain_id = nr[2].upper()
chain_label = f"{pdb_id}_{str(pdb_model)}_{pdb_chain_id}"
res = sql_ask_database(conn, f"""SELECT chain_id from chain
WHERE structure_id='{pdb_id}'
AND chain_name='{pdb_chain_id}'
AND rfam_acc = 'unmappd'
AND issue=0""")
if not len(res) or self.REUSE_ALL: # the chain is NOT yet in the database, or this is a known issue
self.update.append(Chain(pdb_id, pdb_model, pdb_chain_id, chain_label, eq_class))
for rep in representatives:
nr = rep.split('|')
pdb_id = nr[0].lower()
pdb_model = int(nr[1])
pdb_chain_id = nr[2].upper()
chain_label = f"{pdb_id}_{str(pdb_model)}_{pdb_chain_id}"
res = sql_ask_database(conn, f"""SELECT chain_id from chain
WHERE structure_id='{pdb_id}'
AND chain_name='{pdb_chain_id}'
AND rfam_acc = 'unmappd'
AND issue=0""")
if not len(res) or self.REUSE_ALL: # the chain is NOT yet in the database, or this is a known issue
self.update.append(Chain(pdb_id, pdb_model, pdb_chain_id, chain_label, eq_class))
conn.close()
if self.SELECT_ONLY is not None:
......@@ -1491,7 +1399,7 @@ class Pipeline:
else:
mmcif_list = sorted(set([c.pdb_id for c in self.update]))
try:
p = Pool(initializer=init_worker, initargs=(tqdm.get_lock(),), processes=int(coeff_ncores*ncores))
p = Pool(initializer=init_with_tqdm, initargs=(tqdm.get_lock(),), processes=int(coeff_ncores*ncores))
pbar = tqdm(mmcif_list, maxinterval=1.0, miniters=1, desc="mmCIF files")
for _ in p.imap_unordered(work_mmcif, mmcif_list, chunksize=1):
pbar.update(1) # Everytime the iteration finishes, update the global progress bar
......@@ -1539,8 +1447,9 @@ class Pipeline:
args=[c, self.EXTRACT_CHAINS, self.KEEP_HETATM, retry, self.SAVELOGS]))
try:
results = execute_joblist(joblist)
except:
print("Exiting", flush=True)
except Exception as e:
warn(str(e), error=True)
print("Exiting", str(e), flush=True)
exit(1)
# If there were newly discovered problems, add this chain to the known issues
......@@ -1634,7 +1543,11 @@ class Pipeline:
joblist = []
for f in self.fam_list:
# the function already uses all CPUs so launch them one by one (how_many_in_parallel=1)
joblist.append(Job(function=work_realign, args=[self.USESINA, self.ALIGNOPTS, f], how_many_in_parallel=1, label=f))
if f in LSU_set or f in SSU_set:
opts = self.RRNAALIGNOPTS
else:
opts = self.ALIGNOPTS
joblist.append(Job(function=work_realign, args=[self.USESINA, opts, f], how_many_in_parallel=1, label=f))
# Execute the jobs
try:
......@@ -1649,7 +1562,7 @@ class Pipeline:
align = AlignIO.read(path_to_seq_data + "realigned/" + r[0] + "++.afa", "fasta")
nb_3d_chains = len([1 for r in align if '[' in r.id])
if r[0] in SSU_set: # SSU v138.1 is used
nb_homologs = 2224740 # source: https://www.arb-silva.de/documentation/release-1381/
nb_homologs = 2224740 # source: https://www.arb-silva.de/documentation/release-1381/
nb_total_homol = nb_homologs + nb_3d_chains
elif r[0] in LSU_set: # LSU v138.1 is used
nb_homologs = 227331 # source: https://www.arb-silva.de/documentation/release-1381/
......@@ -1684,12 +1597,12 @@ class Pipeline:
# Start a process pool to dispatch the RNA families,
# over multiple CPUs (one family by CPU)
p = Pool(initializer=init_worker, initargs=(tqdm.get_lock(),), processes=nworkers)
p = Pool(initializer=init_with_tqdm, initargs=(tqdm.get_lock(),), processes=nworkers)
try:
fam_pbar = tqdm(total=len(self.fam_list), desc="RNA families", position=0, leave=True)
# Apply work_pssm_remap to each RNA family
for i, _ in enumerate(p.imap_unordered(work_pssm_remap, self.fam_list, chunksize=1)):
for i, _ in enumerate(p.imap_unordered(partial(work_pssm_remap, useSina=pp.USESINA), self.fam_list, chunksize=1)):
# Everytime the iteration finishes on a family, update the global progress bar over the RNA families
fam_pbar.update(1)
fam_pbar.close()
......@@ -1741,10 +1654,10 @@ class Pipeline:
os.makedirs(path_to_3D_data + "datapoints/")
# Save to by-chain CSV files
p = Pool(initializer=init_worker, initargs=(tqdm.get_lock(),), processes=3)
p = Pool(initializer=init_with_tqdm, initargs=(tqdm.get_lock(),), processes=3)
try:
pbar = tqdm(total=len(self.loaded_chains), desc="Saving chains to CSV", position=0, leave=True)
for _, _2 in enumerate(p.imap_unordered(work_save, self.loaded_chains)):
for _, _2 in enumerate(p.imap_unordered(partial(work_save, homology=pp.HOMOLOGY), self.loaded_chains)):
pbar.update(1)
pbar.close()
p.close()
......@@ -1790,18 +1703,28 @@ class Pipeline:
if self.ARCHIVE:
os.makedirs(runDir + "/archive", exist_ok=True)
datestr = time.strftime('%Y%m%d')
# The text files
subprocess.run(["rm", "-f", runDir + f"/archive/RNANET_datapoints_latest.tar.gz"])
subprocess.run(["tar", "-C", path_to_3D_data + "/datapoints", "-czf", runDir + f"/archive/RNANET_datapoints_{datestr}.tar.gz", "."])
subprocess.run(["ln", "-s", runDir + f"/archive/RNANET_datapoints_{datestr}.tar.gz", runDir + f"/archive/RNANET_datapoints_latest.tar.gz"])
# The alignments
if self.HOMOLOGY:
# gather the alignments
os.makedirs(path_to_seq_data + "realigned/3d_only", exist_ok=True)
for f in os.listdir(path_to_seq_data + "realigned"):
if "3d_only.afa" in f:
subprocess.run(["cp", path_to_seq_data + "realigned/" + f, path_to_seq_data + "realigned/3d_only"])
subprocess.run(["rm", "-f", runDir + f"/archive/RNANET_alignments_latest.tar.gz"])
subprocess.run(["tar", "-C", path_to_seq_data + "realigned/3d_only" , "-czf", runDir + f"/archive/RNANET_alignments_latest.tar.gz", "."])
subprocess.run(["rm", "-f", runDir + f"/archive/RNANET_3dOnlyAlignments_latest.tar.gz"])
subprocess.run(["tar", "-C", path_to_seq_data + "realigned/3d_only" , "-czf", runDir + f"/archive/RNANET_3dOnlyAlignments_latest.tar.gz", "."])
# The 3D files
if os.path.isdir(path_to_3D_data + "rna_mapped_to_Rfam"):
subprocess.run(["rm", "-f", runDir + f"/archive/RNANET_MMCIFmappedToRfam_latest.tar.gz"])
subprocess.run(["tar", "-C", path_to_3D_data + "rna_mapped_to_Rfam" , "-czf", runDir + f"/archive/RNANET_MMCIFmappedToRfam_latest.tar.gz", "."])
if os.path.isdir(path_to_3D_data + "rna_only"):
subprocess.run(["rm", "-f", runDir + f"/archive/RNANET_MMCIFall_latest.tar.gz"])
subprocess.run(["tar", "-C", path_to_3D_data + "rna_only" , "-czf", runDir + f"/archive/RNANET_MMCIFall_latest.tar.gz", "."])
def sanitize_database(self):
"""Searches for issues in the database and correct them"""
......@@ -1867,6 +1790,7 @@ class Pipeline:
conn.close()
# ==================== General helper functions =====================
def read_cpu_number():
"""This function reads the number of CPU cores available from /proc/cpuinfo.
......@@ -1876,17 +1800,33 @@ def read_cpu_number():
p = subprocess.run(['grep', '-Ec', '(Intel|AMD)', '/proc/cpuinfo'], stdout=subprocess.PIPE)
return int(int(p.stdout.decode('utf-8')[:-1])/2)
def init_worker(tqdm_lock=None):
def init_with_tqdm(tqdm_lock=None):
"""
This initiation method kills the children when signal is received,
and the children progress is followed using TQDM progress bars.
"""
signal.signal(signal.SIGINT, signal.SIG_IGN)
if tqdm_lock is not None:
tqdm.set_lock(tqdm_lock)
def init_no_tqdm(arg1, arg2, arg3):
"""
This initiaiton method does not kill the children when signal is received,
they will complete and die even after the main process stops.
The children progress is followed using stdout text logs (notify(), warn(), etc)
"""
global n_launched, n_finished, n_skipped
n_launched = arg1
n_finished = arg2
n_skipped = arg3
def warn(message, error=False):
"""Pretty-print warnings and error messages.
"""
Pretty-print warnings and error messages.
"""
# Cut if too long
if len(message) > 66:
x = message.find(' ', 50, 66)
x = message.find(' ', 40, 66)
if x != -1:
warn(message[:x], error=error)
warn(message[x+1:], error=error)
......@@ -1900,20 +1840,133 @@ def warn(message, error=False):
print(f"\t> \033[33mWARN: {message:64s}\033[0m\t{warnsymb}", flush=True)
def notify(message, post=''):
"""
Pretty-print successful finished tasks.
"""
if len(post):
post = '(' + post + ')'
print(f"\t> {message:70s}\t{validsymb}\t{post}", flush=True)
def _mutable_SeqIO_to_alignment_iterator(handle):
records = list(MutableFastaIterator(handle))
if records:
yield MultipleSeqAlignment(records)
# ========================= Biopython overloads =====================
def parse(handle):
with open(handle, 'r') as fp:
yield from _mutable_SeqIO_to_alignment_iterator(fp)
def save_mmcif(ioobj, out_file, select=Select(), preserve_atom_numbering=False):
"""
MMCIF writer which renumbers residues according to the RNANet index_chain (coming from DSSR).
"""
if isinstance(out_file, str):
fp = open(out_file, "w")
close_file = True
else:
fp = out_file
close_file = False
atom_dict = defaultdict(list)
# Iterate on models
for model in ioobj.structure.get_list():
if not select.accept_model(model):
continue
# mmCIF files with a single model have it specified as model 1
if model.serial_num == 0:
model_n = "1"
else:
model_n = str(model.serial_num)
# This is used to write label_entity_id and label_asym_id and
# increments from 1, changing with each molecule
entity_id = 0
if not preserve_atom_numbering:
atom_number = 1
# Iterate on chains
for chain in model.get_list():
if not select.accept_chain(chain):
continue
chain_id = chain.get_id()
if chain_id == " ":
chain_id = "."
# This is used to write label_seq_id, remaining blank for hetero residues
prev_residue_type = ""
prev_resname = ""
# Iterate on residues
for residue in chain.get_unpacked_list():
if not select.accept_residue(residue):
continue
hetfield, resseq, icode = residue.get_id()
if hetfield == " ":
residue_type = "ATOM"
label_seq_id = str(resseq)
else:
residue_type = "HETATM"
label_seq_id = "."
resseq = str(resseq)
if icode == " ":
icode = "?"
resname = residue.get_resname()
# Check if the molecule changes within the chain.
# This will always increment for the first residue in a
# chain due to the starting values above
if residue_type != prev_residue_type or (residue_type == "HETATM" and resname != prev_resname):
entity_id += 1
prev_residue_type = residue_type
prev_resname = resname
label_asym_id = ioobj._get_label_asym_id(entity_id)
# Iterate on atoms
for atom in residue.get_unpacked_list():
if select.accept_atom(atom):
atom_dict["_atom_site.group_PDB"].append(residue_type)
if preserve_atom_numbering:
atom_number = atom.get_serial_number()
atom_dict["_atom_site.id"].append(str(atom_number))
if not preserve_atom_numbering:
atom_number += 1
element = atom.element.strip()
if element == "":
element = "?"
atom_dict["_atom_site.type_symbol"].append(element)
atom_dict["_atom_site.label_atom_id"].append(atom.get_name().strip())
altloc = atom.get_altloc()
if altloc == " ":
altloc = "."
atom_dict["_atom_site.label_alt_id"].append(altloc)
atom_dict["_atom_site.label_comp_id"].append(resname.strip())
atom_dict["_atom_site.label_asym_id"].append(label_asym_id)
# The entity ID should be the same for similar chains
# However this is non-trivial to calculate so we write "?"
atom_dict["_atom_site.label_entity_id"].append("?")
atom_dict["_atom_site.label_seq_id"].append(label_seq_id)
atom_dict["_atom_site.pdbx_PDB_ins_code"].append(icode)
coord = atom.get_coord()
atom_dict["_atom_site.Cartn_x"].append("%.3f" % coord[0])
atom_dict["_atom_site.Cartn_y"].append("%.3f" % coord[1])
atom_dict["_atom_site.Cartn_z"].append("%.3f" % coord[2])
atom_dict["_atom_site.occupancy"].append(str(atom.get_occupancy()))
atom_dict["_atom_site.B_iso_or_equiv"].append(str(atom.get_bfactor()) )
atom_dict["_atom_site.auth_seq_id"].append(resseq)
atom_dict["_atom_site.auth_asym_id"].append(chain_id)
atom_dict["_atom_site.pdbx_PDB_model_num"].append(model_n)
# Data block name is the structure ID with special characters removed
structure_id = ioobj.structure.id
for c in ["#", "$", "'", '"', "[", "]", " ", "\t", "\n"]:
structure_id = structure_id.replace(c, "")
atom_dict["data_"] = structure_id
# Set the dictionary and write out using the generic dictionary method
ioobj.dic = atom_dict
ioobj._save_dict(fp)
if close_file:
fp.close()
def read(handle):
"""
A shortcut to parse alignment files with our custom class MutableFastaIterator.
"""
iterator = parse(handle)
try:
alignment = next(iterator)
......@@ -1926,6 +1979,25 @@ def read(handle):
pass
return alignment
def parse(handle):
"""
A shortcut to parse alignment files with our custom class MutableFastaIterator.
Called by function read().
"""
with open(handle, 'r') as fp:
yield from _mutable_SeqIO_to_alignment_iterator(fp)
def _mutable_SeqIO_to_alignment_iterator(handle):
"""
A shortcut to parse alignment files with our custom class MutableFastaIterator.
Used by the parse() function.
"""
records = list(MutableFastaIterator(handle))
if records:
yield MultipleSeqAlignment(records)
# ========================== SQL related ============================
def sql_define_tables(conn):
conn.executescript(
""" PRAGMA foreign_keys = on;
......@@ -2085,12 +2157,19 @@ def sql_execute(conn, sql, many=False, data=None, warn_every=10):
time.sleep(0.2)
warn("Tried to reach database 100 times and failed. Aborting.", error=True)
# ======================= RNANet Jobs and tasks ======================
@trace_unhandled_exceptions
def execute_job(j, jobcount):
"""Run a Job object.
"""
Run a Job object.
"""
global n_launched, n_skipped, n_finished
# increase the counter of running jobs
running_stats[0] += 1
with n_launched.get_lock():
n_launched.value += 1
# Monitor this process
m = -1
......@@ -2098,7 +2177,7 @@ def execute_job(j, jobcount):
if len(j.cmd_): # The job is a system command
print(f"[{running_stats[0]+running_stats[2]}/{jobcount}]\t{j.label}")
print(f"[{n_launched.value+n_skipped.value}/{jobcount}]\t{j.label}")
# Add the command to logfile
os.makedirs(runDir+"/logs", exist_ok=True)
......@@ -2114,9 +2193,20 @@ def execute_job(j, jobcount):
# run the command. subprocess.run will be a child of this process, and stays monitored.
start_time = time.time()
r = subprocess.run(j.cmd_, timeout=j.timeout_,
stdout=subprocess.PIPE, stderr=subprocess.PIPE)
r = subprocess.run(j.cmd_, timeout=j.timeout_, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
end_time = time.time()
if r.returncode != 0:
if r.stderr is not None:
print(r.stderr, flush=True)
print(f"[{n_launched.value+n_skipped.value}/{jobcount}]\tIssue faced with {j.label}, skipping it and adding it to known issues (if not known).")
with n_launched.get_lock():
n_launched.value -= 1
with n_skipped.get_lock():
n_skipped.value += 1
if j.label not in issues:
issues.add(j.label)
with open("known_issues.txt", "a") as iss:
iss.write(j.label+"\n")
# Stop the Monitor, then get its result
monitor.keep_watching = False
......@@ -2124,7 +2214,7 @@ def execute_job(j, jobcount):
elif j.func_ is not None:
print(f"[{running_stats[0]+running_stats[2]}/{jobcount}]\t{j.func_.__name__}({', '.join([str(a) for a in j.args_ if type(a) != list])})", flush=True)
print(f"[{n_launched.value+n_skipped.value}/{jobcount}]\t{j.func_.__name__}({', '.join([str(a) for a in j.args_ if type(a) != list])})", flush=True)
with concurrent.futures.ThreadPoolExecutor(max_workers=1) as executor:
# put the monitor in a different thread
......@@ -2140,7 +2230,8 @@ def execute_job(j, jobcount):
m = assistant_future.result()
# increase the counter of finished jobs
running_stats[1] += 1
with n_finished.get_lock():
n_finished.value += 1
# return time and memory statistics, plus the job results
t = end_time - start_time
......@@ -2155,9 +2246,12 @@ def execute_joblist(fulljoblist):
"""
# Reset counters
running_stats[0] = 0 # started
running_stats[1] = 0 # finished
running_stats[2] = 0 # failed
with n_launched.get_lock():
n_launched.value = 0
with n_skipped.get_lock():
n_skipped.value = 0
with n_finished.get_lock():
n_finished.value = 0
# Sort jobs in a tree structure, first by priority, then by CPU numbers
jobs = {}
......@@ -2193,21 +2287,21 @@ def execute_joblist(fulljoblist):
print("using", n, "processes:")
# execute jobs of priority i that should be processed n by n:
p = Pool(processes=n, maxtasksperchild=1, initializer=init_worker)
p = Pool(processes=n, maxtasksperchild=1, initializer=init_no_tqdm, initargs=(n_launched, n_finished, n_skipped))
try:
raw_results = p.map(partial(execute_job, jobcount=jobcount), bunch, chunksize=2)
p.close()
p.join()
except KeyboardInterrupt as e:
warn("KeyboardInterrupt, killing workers (SIGKILL).", error=True)
p.kill()
p.terminate()
p.join()
raise e
for j, r in zip(bunch, raw_results):
j.comp_time = round(r[0], 2) # seconds
j.max_mem = int(r[1]/1000000) # MB
results.append((j.label, r[2], round(r[0], 2), int(r[1]/1000000)))
results.append((j.label, r[2], j.comp_time, j.max_mem))
# throw back the money
return results
......@@ -2235,7 +2329,7 @@ def work_infer_mappings(update_only, allmappings, fullinference, redundant, code
# Split the comma-separated list of chain codes into chain codes:
eq_class = codelist[0]
codes = codelist[2].replace('+', ',').split(',')
representative=codelist[1].replace('+', ',').split(',')[0]
representative = codelist[1].replace('+', ',').split(',')[0]
# Search for mappings that apply to an element of this PDB chains list:
for c in codes:
# search for Rfam mappings with this chain c:
......@@ -2394,7 +2488,20 @@ def work_mmcif(pdb_id):
# if not, read the CIF header and register the structure
if not len(r):
# Load the MMCIF file with Biopython
mmCif_info = pdb.MMCIF2Dict.MMCIF2Dict(final_filepath)
try:
mmCif_info = pdb.MMCIF2Dict.MMCIF2Dict(final_filepath)
except ValueError:
# mmcif file is empty or wrong. This happens when you interrupt RNANet while it
# downloads. Retry to download it properly.
subprocess.run(
["wget", f'http://files.rcsb.org/download/{pdb_id}.cif', "-O", final_filepath],
stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL
)
try:
mmCif_info = pdb.MMCIF2Dict.MMCIF2Dict(final_filepath)
except ValueError:
warn(f"Empty or wrong {final_filepath.split('/')[-1]} file. Ignoring this structure.")
return 1
# Get info about that structure
try:
......@@ -2597,20 +2704,41 @@ def use_infernal(rfam_acc, alignopts):
new_ali_path = path_to_seq_data + f"realigned/{rfam_acc}_new.stk"
# Align the new sequences
with open(new_ali_path, 'w') as o:
p1 = subprocess.run(["cmalign", "--ifile", path_to_seq_data + f"realigned/{rfam_acc}.ins",
with open(path_to_seq_data + f"realigned/{rfam_acc}_new.log", 'w') as o:
cmd = ["cmalign"]
if alignopts is not None:
cmd += alignopts
p1 = subprocess.run(cmd + ["--ifile", path_to_seq_data + f"realigned/{rfam_acc}.ins",
"--sfile", path_to_seq_data + f"realigned/{rfam_acc}.tsv",
"-o", path_to_seq_data + f"realigned/{rfam_acc}++.stk",
"-o", new_ali_path,
path_to_seq_data + f"realigned/{rfam_acc}.cm",
path_to_seq_data + f"realigned/{rfam_acc}_new.fa"],
stdout=o, stderr=subprocess.PIPE)
align_errors = p1.stderr.decode("utf-8")
if len(align_errors):
if "--mxsize" in align_errors:
# not enough available RAM to allocate the DP matrix
warn(f"Not enough RAM to allocate cmalign DP matrix for family {rfam_acc}. Use --sina or --cmalign-opts.", error=True)
else:
warn(align_errors, error=True)
return
notify("Aligned new sequences together")
# Detect doublons and remove them
existing_stk = AlignIO.read(existing_ali_path, "stockholm")
try:
existing_stk = AlignIO.read(existing_ali_path, "stockholm")
except ValueError:
# Not a stockholm file
warn(f"Existing alignment is not a Stockholm file !", error=True)
return
existing_ids = [r.id for r in existing_stk]
del existing_stk
new_stk = AlignIO.read(new_ali_path, "stockholm")
try:
new_stk = AlignIO.read(new_ali_path, "stockholm")
except ValueError:
# Not a stockholm file
warn(f"New alignment {new_ali_path} is not a Stockholm file !", error=True)
return
new_ids = [r.id for r in new_stk]
del new_stk
doublons = [i for i in existing_ids if i in new_ids]
......@@ -2629,7 +2757,11 @@ def use_infernal(rfam_acc, alignopts):
p2 = subprocess.run(["esl-alimerge", "-o", path_to_seq_data + f"realigned/{rfam_acc}_merged.stk",
"--rna", existing_ali_path, new_ali_path],
stdout=subprocess.DEVNULL, stderr=subprocess.PIPE)
stderr = p1.stderr.decode('utf-8') + p2.stderr.decode('utf-8')
alignErrors = p1.stderr.decode('utf-8')
mergeErrors = p2.stderr.decode('utf-8')
alignErrors = "Alignment: "+ alignErrors if len(alignErrors) else ""
mergeErrors = "Alignment: "+ mergeErrors if len(mergeErrors) else ""
stderr = alignErrors + mergeErrors
subprocess.run(["mv", path_to_seq_data + f"realigned/{rfam_acc}_merged.stk", existing_ali_path])
notify("Merged alignments into one")
......@@ -2642,7 +2774,7 @@ def use_infernal(rfam_acc, alignopts):
cmd = ["cmalign"]
if alignopts is not None:
cmd += " ".split(alignopts)
cmd += alignopts
cmd += ['-o', path_to_seq_data + f"realigned/{rfam_acc}++.stk",
"--ifile", path_to_seq_data + f"realigned/{rfam_acc}.ins",
"--sfile", path_to_seq_data + f"realigned/{rfam_acc}.tsv",
......@@ -2663,8 +2795,8 @@ def use_infernal(rfam_acc, alignopts):
# Convert Stockholm to aligned FASTA
subprocess.run(["esl-reformat", "-o", path_to_seq_data + f"realigned/{rfam_acc}++.afa",
"--informat", "stockholm",
"afa", path_to_seq_data + f"realigned/{rfam_acc}++.stk"])
"--informat", "stockholm",
"afa", path_to_seq_data + f"realigned/{rfam_acc}++.stk"])
subprocess.run(["rm", "-f", "esltmp*"]) # We can use a joker here, because we are not running in parallel for this part.
@trace_unhandled_exceptions
......@@ -2708,7 +2840,7 @@ def work_save_pydca(f,alignment):
warn(e)
@trace_unhandled_exceptions
def work_pssm_remap(f):
def work_pssm_remap(f, useSina=False):
"""Computes Position-Specific-Scoring-Matrices given the multiple sequence alignment of the RNA family.
This also remaps the 3D object sequence with the aligned sequence in the MSA.
If asked, the 3D object sequence is completed by the consensus nucleotide when one of them is missing.
......@@ -2890,7 +3022,7 @@ def work_pssm_remap(f):
setproctitle(f"RNAnet.py work_pssm_remap({f}) insert/match states")
# Get back the information of match/insertion states from the STK file
if (not use_sina) or (f not in SSU_set and f not in LSU_set):
if (not useSina) or (f not in SSU_set and f not in LSU_set):
alignstk = AlignIO.read(path_to_seq_data + "realigned/" + f + "++.stk", "stockholm")
consensus_2d = alignstk.column_annotations["secondary_structure"]
del alignstk
......@@ -2936,8 +3068,6 @@ def work_pssm_remap(f):
gap_percent, consensus, cons_sec_struct)
VALUES (?, 0, 0, NULL, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0, '-', NULL);""", data=(f,))
# Save the number of "used columns" to table family ( = the length of the alignment if it was composed only of the RNANet chains)
sql_execute(conn, f"UPDATE family SET ali_filtered_len = ? WHERE rfam_acc = ?;", data=(len(columns_to_save), f))
conn.close()
......@@ -3021,6 +3151,8 @@ def work_save(c, homology=True):
df.to_csv(filename, float_format="%.2f", index=False)
# =========================== Main function =============================
if __name__ == "__main__":
fileDir = os.path.dirname(os.path.realpath(__file__))
......@@ -3068,17 +3200,9 @@ if __name__ == "__main__":
print(f"Among errors, {len(no_nts_set)} structures seem to contain RNA chains without defined nucleotides:", no_nts_set, flush=True)
if len(weird_mappings):
print(f"{len(weird_mappings)} mappings to Rfam were taken as absolute positions instead of residue numbers:", weird_mappings, flush=True)
if pp.SELECT_ONLY is None:
if pp.HOMOLOGY and pp.SELECT_ONLY is None:
pp.checkpoint_save_chains()
if not pp.HOMOLOGY:
# Save chains to file
for c in pp.loaded_chains:
work_save(c, homology=False)
print("Completed.")
exit(0)
# At this point, structure, chain and nucleotide tables of the database are up to date.
# (Modulo some statistics computed by statistics.py)
......@@ -3086,33 +3210,34 @@ if __name__ == "__main__":
# Homology information
# ===========================================================================
if pp.SELECT_ONLY is None:
# If your job failed, you can comment all the "3D information" part and start from here.
pp.checkpoint_load_chains()
if pp.HOMOLOGY:
if pp.SELECT_ONLY is None:
# If your job failed, you can comment all the "3D information" part and start from here.
pp.checkpoint_load_chains()
# Get the list of Rfam families found in the update
rfam_acc_to_download = {}
for c in pp.loaded_chains:
if c.mapping.rfam_acc not in rfam_acc_to_download.keys():
rfam_acc_to_download[c.mapping.rfam_acc] = [c]
else:
rfam_acc_to_download[c.mapping.rfam_acc].append(c)
# Get the list of Rfam families found in the update
rfam_acc_to_download = {}
for c in pp.loaded_chains:
if c.mapping.rfam_acc not in rfam_acc_to_download.keys():
rfam_acc_to_download[c.mapping.rfam_acc] = [c]
else:
rfam_acc_to_download[c.mapping.rfam_acc].append(c)
print(f"> Identified {len(rfam_acc_to_download.keys())} families to update and re-align with the crystals' sequences")
pp.fam_list = sorted(rfam_acc_to_download.keys())
print(f"> Identified {len(rfam_acc_to_download.keys())} families to update and re-align with the crystals' sequences")
pp.fam_list = sorted(rfam_acc_to_download.keys())
if len(pp.fam_list):
pp.prepare_sequences()
pp.realign()
if len(pp.fam_list):
pp.prepare_sequences()
pp.realign()
# At this point, the family table is almost up to date
# (lacking idty_percent and ali_filtered_length, both set in statistics.py)
# At this point, the family table is almost up to date
# (lacking idty_percent and ali_filtered_length, both set in statistics.py)
thr_idx_mgr = Manager()
idxQueue = thr_idx_mgr.Queue()
thr_idx_mgr = Manager()
idxQueue = thr_idx_mgr.Queue()
pp.remap()
pp.extractCMs()
pp.remap()
pp.extractCMs()
# At this point, the align_column and re_mapping tables are up-to-date.
......
# Warnings and errors in RNANet
Use Ctrl + F on this page to look for your error message in the list.
......@@ -27,7 +26,7 @@ DSSR complains because the CIF structure does not seem to contain nucleotides. T
* **Error downloading and/or extracting Rfam.cm !** : We cannot retrieve the Rfam covariance models file. RNANet tries to find it at ftp://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/Rfam.cm.gz so, check that your network is not blocking the FTP protocol (port 21 is open on your network), and check that the adress has not changed. If so, contact us so that we update RNANet with the correct address.
* **Something's wrong with the SQL database. Check mysql-rfam-public.ebi.ac.uk status and try again later. Not printing statistics.** : We cannot retrieve family statistics from Rfam public server. Check if you can connect to it by hand : `mysql -u rfamro -P 4497 -D Rfam -h mysql-rfam-public.ebi.ac.uk`. if not, check that the port 497 is opened on your network.
* **Something's wrong with the SQL database. Check mysql-rfam-public.ebi.ac.uk status and try again later. Not printing statistics.** : We cannot retrieve family statistics from Rfam public server. Check if you can connect to it by hand : `mysql -u rfamro -P 4497 -D Rfam -h mysql-rfam-public.ebi.ac.uk`. if not, check that the port 4497 is opened on your network.
* **Error downloading RFXXXXX.fa.gz: {custom-error}** : We cannot reach the Rfam FTP server to download homologous sequences. We look in ftp://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/fasta_files/ so, check if you can access it from your network (check that port 21 is opened on your network). Check if the address has changed and notify us.
......
......@@ -7,6 +7,15 @@ In `cmalign` alignments, - means a nucleotide is missing compared to the covaria
In the final filtered alignment that we provide for download, the same rule applies, but on top of that, some '.' are replaced by '-' when a gap in the 3D structure (a missing, unresolved nucleotide) is mapped to an insertion gap.
* **What are the cmalign options for ?**
From Infernal's user guide, we can quote that Infernal uses an HMM banding technique to accelerate alignment by default. It also takes care of 3' or 5' truncated sequences to be aligned correctly (and we have some).
First, one can choose an algorithm, between `--optacc` (maximizing posterior probabilities, the default) and `--cyk` (maximizing likelihood).
Then, the use of bands allows faster and more memory efficient computation, at the price of the guarantee of determining the optimal alignment. Bands can be disabled using the `--nonbanded` option. A best idea would be to control the threshold of probability mass to be considered negligible during HMM band calculation with the `--tau` parameter. Higher values of Tau yield greater speedups and lower memory usage, but a greater chance to miss the optimal alignment. In practice, the algorithm explores several Tau values (increasing it by a factor 2.0 from the original `--tau` value) until the DP matrix size falls below the threshold given by `--mxsize` (default 1028 Mb) or the value of `--maxtau` is reached (in this case, the program fails). One can disable this exploration with option `--fixedtau`. The default value of `--tau` is 1e-7, the default `--maxtau` is 0.05. Basically, you may decide on a value of `--mxsize` by dividing your available RAM by the number of cores used with cmalign. If necessary, you may use less cores than you have, using option `--cpu`.
Finally, if using `--cyk --nonbanded --notrunc --noprob`, one can use the `--small` option to align using the divide-and-conquer CYK algorithm from Eddy 2002, requiring a very few memory but a lot of time. The major drawback of this is that it requires `--notrunc` and `--noprob`, so we give up on the correct alignment of truncated sequences, and the computation of posterior probabilities.
* **Why are there some gap-only columns in the alignment ?**
These columns are not completely gap-only, they contain at least one dash-gap '-'. This means an actual, physical nucleotide which should exist in the 3D structure should be located there. The previous and following nucleotides are **not** contiguous in space in 3D.
......@@ -31,5 +40,5 @@ We first remove the nucleotides whose number is outside the family mapping (if a
* **What are the versions of the dependencies you use ?**
`cmalign` is v1.1.4, `sina` is v1.6.0, `x3dna-dssr` is v1.9.9, Biopython is v1.78.
`cmalign` is v1.1.4, `sina` is v1.6.0, `x3dna-dssr` is v2.3.2-2021jun29, Biopython is v1.78.
\ No newline at end of file
......
* [Required computational resources](#required-computational-resources)
* [Required hardware resources](#required-computational-resources)
* [Method 1 : Using Docker](#method-1-:-installation-using-docker)
* [Method 2 : Classical command-line installation](#method-2-:-classical-command-line-installation-linux-only)
* [Command options](#command-options)
......@@ -7,19 +7,29 @@
* [Post-computation tasks](#post-computation-tasks-estimate-quality)
* [Output files](#output-files)
# Required computational resources
- CPU: no requirements. The program is optimized for multi-core CPUs, you might want to use Intel Xeons, AMD Ryzens, etc.
- GPU: not required
- RAM: 16 GB with a large swap partition is okay. 32 GB is recommended (usage peaks at ~27 GB, but this number depends on your number of CPU cores)
- Storage: to date, it takes 60 GB for the 3D data (36 GB if you don't use the --extract option), 11 GB for the sequence data, and 7GB for the outputs (5.6 GB database, 1 GB archive of CSV files). You need to add a few more for the dependencies. Pick a 100GB partition and you are good to go. The computation speed is way better if you use a fast storage device (e.g. SSD instead of hard drive, or even better, a NVMe SSD) because of constant I/O with the SQlite database.
- Network : We query the Rfam public MySQL server on port 4497. Make sure your network enables communication (there should not be any issue on private networks, but maybe you company/university closes ports by default). You will get an error message if the port is not open. Around 30 GB of data is downloaded.
# Required hardware resources
- **CPU**: The program is optimized for highly multi-core CPUs. The more you have, the faster the computation. Ensure you have enough RAM to follow.
- **GPU**: not required.
- **RAM**: This depends on the usage.
- In regular mode, the first computation of alignments requires a huge 100GB. If you do not have them, you might:
- either want to use SINA (--sina) instead of Infernal to align the rRNAs. However, all information related to covariance models will not be available for them (distance matrices, 3D-only alignments...)
- or customize options --cmalign-opts and --cmalign-rrna-opts with cmalign arguments --cpu (number of cores to use) and --mxsize (max memory to allocate per core), so that it fits your machine. In very hard cases, also increase the parameter --maxtau from 0.05 to 0.1, but this reduces the quality of the alignments.
- In regular "update" mode, when the alignments already exists, less RAM is required, 64GB should be fine. If not, use the same options than the first time for your update runs.
- In 'no homology' mode, just for annotation of the structures without mapping to families, each core can peak to ~3GB (but not all at the same time if you are lucky). Use option --maxcores to reduce the number of cores if you do not have enough RAM. 32GB is fine in most cases.
- **Storage**: to date, it takes 60 GB for the 3D data (36 GB if you don't use the --extract option), 11 GB for the sequence data, and 7GB for the outputs (5.6 GB database, 1 GB archive of CSV files). You need to add a few more for the dependencies. If you compute geometry statistics and parameter distributions, you need to count a 80GB more (permanent) and 100GB more (that will be deleted at the end of the run). So, pick a 250GB partition and you are good to go. The computation speed is much higher if you use a fast storage device (e.g. SSD instead of hard drive, or even better, a NVMe M.2) because of constant I/O with the SQlite database.
- **Network** : We query the Rfam public MySQL server on port 4497. Make sure your network enables communication (there should not be any issue on private networks, but your university may close ports by default). You will get an error message if the port is not open. Around 30 GB of data is downloaded.
The IBISC-EvryRNA server example :
* Intel Xeon E7-4850 v4 (60 cores, 2.10GHz)
* 112 GB of RAM
* 250 GB of hard-disk storage
# Method 1 : Installation using Docker
* Step 1 : Download the [Docker container](https://entrepot.ibisc.univ-evry.fr/d/1aff90a9ef214a19b848/files/?p=/rnanet_v1.5b_docker.tar&dl=1). Open a terminal and move to the appropriate directory.
* Step 1 : Download the [Docker container](https://entrepot.ibisc.univ-evry.fr/d/1aff90a9ef214a19b848/files/?p=/rnanet_v1.6b_docker.tar&dl=1). Open a terminal and move to the appropriate directory.
* Step 2 : Extract the archive to a Docker image named *rnanet* in your local installation
```
$ docker load -i rnanet_v1.5b_docker.tar
$ docker load -i rnanet_v1.6b_docker.tar
```
* Step 3 : Run the container, giving it 3 folders to mount as volumes: a first to store the 3D data, a second to store the sequence data and alignments, and a third to output the results, data and logs:
```
......@@ -35,11 +45,11 @@ nohup bash -c 'time docker run --rm -v /path/to/3D/data/folder:/3D -v /path/to/s
# Method 2 : Classical command line installation (Linux only)
You need to install the dependencies:
- DSSR, you need to register to the X3DNA forum [here](http://forum.x3dna.org/site-announcements/download-instructions/) and then download the DSSR binary [on that page](http://forum.x3dna.org/downloads/3dna-download/). Make sure to have the `x3dna-dssr` binary in your $PATH variable so that RNANet.py finds it.
- Infernal, to download at [Eddylab](http://eddylab.org/infernal/), several options are available depending on your preferences. Make sure to have the `cmalign`, `cmfetch`, `cmbuild`, `esl-alimanip`, `esl-alipid` and `esl-reformat` binaries in your $PATH variable, so that RNANet.py can find them.
- SINA, follow [these instructions](https://sina.readthedocs.io/en/latest/install.html) for example. Make sure to have the `sina` binary in your $PATH.
- DSSR 1.9.9 or newer, you need to register to ask for a DSSR (academic) license [on that page](http://innovation.columbia.edu/technologies/CU20391). Make sure to have the `x3dna-dssr` binary in your $PATH variable so that RNANet.py finds it.
- Infernal 1.1.4 or newer, to download at [Eddylab](http://eddylab.org/infernal/), several options are available depending on your preferences. Make sure to have the `cmalign`, `cmfetch`, `cmbuild`, `esl-alimanip`, `esl-alimerge`, `esl-alipid` and `esl-reformat` binaries in your $PATH variable, so that RNANet.py can find them.
- SINA (if you plan to use it), follow [these instructions](https://sina.readthedocs.io/en/latest/install.html) for example. Make sure to have the `sina` binary in your $PATH.
- Sqlite 3, available under the name *sqlite* in every distro's package manager,
- Python >= 3.8, (Unfortunately, python3.6 is no longer supported, because of changes in the multiprocessing and Threading packages. Untested with Python 3.7.\*)
- Python >= 3.8, (Unfortunately, python3.6 is no longer supported, because of changes in the multiprocessing and Threading packages. Untested with Python 3.7.\*).
- The following Python packages: `python3.8 -m pip install biopython matplotlib pandas psutil pymysql requests scipy setproctitle sqlalchemy tqdm`.
Then, run it from the command line, preferably using nohup if your shell will be interrupted:
......@@ -57,50 +67,52 @@ nohup bash -c 'time ~/Projects/RNANet/RNAnet.py --3d-folder ~/Data/RNA/3D/ --seq
The detailed list of options is below:
```
-h [ --help ] Print this help message
--version Print the program version
-h [ --help ] Print this help message
--version Print the program version
Select what to do:
--------------------------------------------------------------------------------------------------------------
-f [ --full-inference ] Infer new mappings even if Rfam already provides some. Yields more copies of
chains mapped to different families.
-s Run statistics computations after completion
--stats-opts=… Pass additional command line options to the statistics.py script, e.g. "--wadley --distance-matrices"
--extract Extract the portions of 3D RNA chains to individual mmCIF files.
--keep-hetatm=False (True | False) Keep ions, waters and ligands in produced mmCIF files.
Does not affect the descriptors.
--no-homology Do not try to compute PSSMs and do not align sequences.
Allows to yield more 3D data (consider chains without a Rfam mapping).
-f [ --full-inference ] Infer new mappings even if Rfam already provides some. Yields more copies of
chains mapped to different families.
-s Run statistics computations after completion
--stats-opts=… Pass additional command line options to the statistics.py script, e.g. "--wadley --distance-matrices"
--extract Extract the portions of 3D RNA chains to individual mmCIF files.
--keep-hetatm=False (True | False) Keep ions, waters and ligands in produced mmCIF files.
Does not affect the descriptors.
--no-homology Do not try to compute PSSMs and do not align sequences.
Allows to yield more 3D data (consider chains without a Rfam mapping).
Select how to do it:
--------------------------------------------------------------------------------------------------------------
--3d-folder=… Path to a folder to store the 3D data files. Subfolders will contain:
RNAcifs/ Full structures containing RNA, in mmCIF format
rna_mapped_to_Rfam/ Extracted 'pure' portions of RNA chains mapped to families
rna_only/ Extracted 'pure' RNA chains, not truncated
datapoints/ Final results in CSV file format.
--seq-folder=… Path to a folder to store the sequence and alignment files. Subfolders will be:
rfam_sequences/fasta/ Compressed hits to Rfam families
realigned/ Sequences, covariance models, and alignments by family
--sina Align large subunit LSU and small subunit SSU ribosomal RNA using SINA instead of Infernal,
the other RNA families will be aligned using infernal.
--maxcores=… Limit the number of cores to use in parallel portions to reduce the simultaneous
need of RAM. Should be a number between 1 and your number of CPUs. Note that portions
of the pipeline already limit themselves to 50% or 70% of that number by default.
--cmalign-opts=… A string of additional options to pass to cmalign aligner, e.g. "--nonbanded --mxsize 2048"
--archive Create tar.gz archives of the datapoints text files and the alignments,
and update the link to the latest archive.
--no-logs Do not save per-chain logs of the numbering modifications.
--3d-folder=… Path to a folder to store the 3D data files. Subfolders will contain:
RNAcifs/ Full structures containing RNA, in mmCIF format
rna_mapped_to_Rfam/ Extracted 'pure' portions of RNA chains mapped to families
rna_only/ Extracted 'pure' RNA chains, not truncated
datapoints/ Final results in CSV file format.
--seq-folder=… Path to a folder to store the sequence and alignment files. Subfolders will be:
rfam_sequences/fasta/ Compressed hits to Rfam families
realigned/ Sequences, covariance models, and alignments by family
--sina Align large subunit LSU and small subunit SSU ribosomal RNA using SINA instead of Infernal,
the other RNA families will be aligned using infernal.
--maxcores=… Limit the number of cores to use in parallel portions to reduce the simultaneous
need of RAM. Should be a number between 1 and your number of CPUs. Note that portions
of the pipeline already limit themselves to 50% or 70% of that number by default.
--cmalign-opts=… A string of additional options to pass to cmalign aligner, e.g. "--nonbanded --mxsize 2048"
--cmalign-rrna-opts=… Like cmalign-opts, but applied for rRNA (large families, memory-heavy jobs).
--archive Create tar.gz archives of the datapoints text files and the alignments,
and update the link to the latest archive.
--no-logs Do not save per-chain logs of the numbering modifications.
Select which data we are interested in:
--------------------------------------------------------------------------------------------------------------
-r 4.0 [ --resolution=4.0 ] Maximum 3D structure resolution to consider a RNA chain.
--all Process chains even if they already are in the database.
--redundant Process all members of the equivalence classes not only the representative.
--only Ask to process a specific chains only (e.g. 4v49, 4v49_1_AA, or 4v49_1_AA_5-1523).
--ignore-issues Do not ignore already known issues and attempt to compute them.
--update-homologous Re-download Rfam and SILVA databases, realign all families, and recompute all CSV files.
--from-scratch Delete database, local 3D and sequence files, and known issues, and recompute.
-r 4.0 [ --resolution=4.0 ] Maximum 3D structure resolution to consider a RNA chain.
--all Process chains even if they already are in the database.
--redundant Process all members of the equivalence classes not only the representative.
--only Ask to process a specific chains only (could be 4v49, 4v49_1_AA, or 4v49_1_AA_5-1523).
--ignore-issues Do not ignore already known issues and attempt to compute them.
--update-homologous Re-download Rfam and SILVA databases, realign all families, and recompute all CSV files.
--from-scratch Delete database, local 3D and sequence files, and known issues, and recompute.
```
Options --3d-folder and --seq-folder are mandatory for command-line installations, but should not be used for installations with Docker. In the Docker container, they are set by default to the paths you provide with the -v options.
......
# Known Issues
## Annotation and numbering issues
* Some GDPs that are listed as HETATMs in the mmCIF files are not detected correctly to be real nucleotides. (e.g. 1e8o-E)
* [SOLVED] Some GDPs that are listed as HETATMs in the mmCIF files are not detected correctly to be real nucleotides. (e.g. 1e8o-E)
* Some chains are truncated in different pieces with different chain names. Reason unknown (e.g. 6ztp-AX)
* Some chains are not correctly renamed A in the produced separate files (e.g. 1d4r-B)
* [SOLVED] Some chains are not correctly renamed A in the produced separate files (e.g. 1d4r-B)
## Alignment issues
* [SOLVED] Filtered alignments are shorter than the number of alignment columns saved to the SQL table `align_column`
* Chain names appear in triple in the FASTA header (e.g. 1d4r[1]-B 1d4r[1]-B 1d4r[1]-B)
## Technical running issues
* [SOLVED] Files produced by Docker containers are owned by root and require root permissions to be read
* [SOLVED] SQLite WAL files are not deleted properly
* [SOLVED] Chain names appear in triple in the FASTA header (e.g. 1d4r[1]-B 1d4r[1]-B 1d4r[1]-B)
# Known feature requests
* [DONE] Get filtered versions of the sequence alignments containing the 3D chains, publicly available for download
* [DONE] Get a consensus residue for each alignement column
* [DONE] Get an option to limit the number of cores
* [DONE] Move to SILVA LSU release 138.1
* [UPCOMING] Automated annotation of detected Recurrent Interaction Networks (RINs), see http://carnaval.lri.fr/ .
* [UPCOMING] Possibly, automated detection of HLs and ILs from the 3D Motif Atlas (BGSU). Maybe. Their own website already does the job.
* [UPCOMING] Weight sequences in alignment to give more importance to rarer sequences
* [UPCOMING] Give both gap_percent and insertion_gap_percent
* Automated annotation of detected Recurrent Interaction Networks (RINs), see http://carnaval.lri.fr/ .
* Possibly, automated detection of HLs and ILs from the 3D Motif Atlas (BGSU). Maybe. Their own website already does the job.
* Weight sequences in alignment to give more importance to rarer sequences
* Give both gap_percent and insertion_gap_percent
* A field estimating the quality of the sequence alignment in table family.
* Possibly, more metrics about the alignments coming from Infernal.
* Run cmscan ourselves from the NDB instead of using Rfam-PDB mappings ? (Iff this actually makes a real difference, untested yet)
* Use and save Infernal alignment bounds and truncation information
* Save if a chain is a representative or not in BGSU list, so that they can be filtered easily
* Annotate unstructured regions (on a nucleotide basis)
## Technical to-do list
* `cmalign --merge` is now deprecated, we use `esl-alimerge` instead. But, esl is a single-core process. We should run the merges of alignements of different families in parallel to save some time [TODO].
......
This diff could not be displayed because it is too large.
6ydp_1_AA_1176-2737
6ydw_1_AA_1176-2737
2z9q_1_A_1-72
1ml5_1_b_5-121
1ml5_1_a_1-2914
3ep2_1_Y_1-72
3eq3_1_Y_1-72
4v48_1_A6_1-73
1ml5_1_A_2-1520
1qzb_1_B_1-73
1qza_1_B_1-73
1ls2_1_B_1-73
1gsg_1_T_1-72
7d1a_1_A_805-902
7d0g_1_A_805-913
7d0f_1_A_817-913
3jcr_1_H_1-115
1vy7_1_AY_1-73
1vy7_1_CY_1-73
4w2h_1_CY_1-73
5zzm_1_M_3-118
2rdo_1_A_3-118
4v48_1_A9_3-118
4v47_1_A9_3-118
2ob7_1_A_10-319
1x1l_1_A_1-130
1zc8_1_Z_1-91
2ob7_1_D_1-130
4v42_1_BA_1-2914
4v42_1_BB_5-121
1r2x_1_C_1-58
1r2w_1_C_1-58
1eg0_1_L_1-56
3dg2_1_A_1-1542
3dg0_1_A_1-1542
4v48_1_BA_1-1543
4v47_1_BA_1-1542
3dg4_1_A_1-1542
3dg5_1_A_1-1542
5zzm_1_N_1-2903
2rdo_1_B_1-2904
3dg2_1_B_1-2904
3dg0_1_B_1-2904
4v48_1_A0_1-2904
4v47_1_A0_1-2904
3dg4_1_B_1-2904
3dg5_1_B_1-2904
1eg0_1_O_1-73
1zc8_1_A_1-59
1jgq_1_A_2-1520
4v42_1_AA_2-1520
1jgo_1_A_2-1520
1jgp_1_A_2-1520
1mvr_1_D_1-59
4c9d_1_D_29-1
4c9d_1_C_29-1
4adx_1_9_1-121
1zn1_1_B_1-59
1emi_1_B_1-108
3iy9_1_A_498-1027
3ep2_1_B_1-50
3eq3_1_B_1-50
3eq4_1_B_1-50
3pgw_1_R_1-164
3pgw_1_N_1-164
3cw1_1_x_1-138
3cw1_1_w_1-138
3cw1_1_V_1-138
3cw1_1_v_1-138
2iy3_1_B_9-105
3jcr_1_N_1-106
2vaz_1_A_64-177
2ftc_1_R_81-1466
3jcr_1_M_1-141
4v5z_1_B0_1-2902
5g2x_1_A_595-692
3iy8_1_A_1-540
4v5z_1_BY_2-113
4v5z_1_BZ_1-70
4v5z_1_B1_2-123
1mvr_1_B_1-96
4adx_1_0_1-2923
3eq4_1_Y_1-69
7a5p_1_2_259-449
6uz7_1_8_2140-2825
4v5z_1_AA_1-1563
6cfj_1_1X
6cfj_1_2X
5hcq_1_1X
......@@ -196,7 +110,6 @@
5lzb_1_V
6h58_1_W
6h58_1_WW
1eg0_1_O
5j8b_1_X
4v7j_1_AV
4v7j_1_BV
......@@ -224,10 +137,6 @@
7k00_1_B
6ys3_1_A
6qdw_1_A
5zzm_1_M
2rdo_1_A
4v48_1_A9
4v47_1_A9
6hcj_1_Q3
6hcq_1_Q3
6o8w_1_U
......@@ -295,7 +204,12 @@
6ucq_1_2Y
4w2e_1_X
6ucq_1_2X
7n1p_1_DT
7n2u_1_DT
6yss_1_W
7n30_1_DT
7n31_1_DT
7n2c_1_DT
5afi_1_Y
5uq8_1_Z
5wdt_1_Y
......@@ -321,18 +235,20 @@
4v4i_1_Y
5uq8_1_X
5uq7_1_X
1jgq_1_A
4v42_1_AA
1jgo_1_A
1jgp_1_A
4v4j_1_W
4v4i_1_W
4v42_1_BA
4wt8_1_CS
4wt8_1_DS
4v4j_1_X
4v4i_1_X
4v42_1_BB
6lkq_1_S
5h5u_1_H
7d6z_1_F
5lze_1_Y
5lze_1_V
5lze_1_X
3jcj_1_G
6o7k_1_G
6d30_1_C
6j7z_1_C
3er9_1_D
......@@ -367,20 +283,11 @@
4oq9_1_1
6rt5_1_A
6rt5_1_E
4qu6_1_B
6lkq_1_T
6ys3_1_B
6qdw_1_B
3jbv_1_B
3jbu_1_B
5zzm_1_N
2rdo_1_B
3dg2_1_B
3dg0_1_B
4v48_1_A0
4v47_1_A0
3dg4_1_B
3dg5_1_B
6do8_1_B
6dpi_1_B
6dp9_1_B
......@@ -437,25 +344,17 @@
6doc_1_B
6doe_1_B
6n6g_1_D
6lkq_1_S
5h5u_1_H
7d6z_1_F
5lze_1_Y
5lze_1_V
5lze_1_X
3jcj_1_G
6o7k_1_G
3dg2_1_A
3dg0_1_A
4v48_1_BA
4v47_1_BA
3dg4_1_A
3dg5_1_A
4b3r_1_W
4b3t_1_W
4b3s_1_W
7b5k_1_X
5o2r_1_X
5kcs_1_1X
7n1p_1_PT
7n2u_1_PT
7n30_1_PT
7n31_1_PT
7n2c_1_PT
6zvk_1_E2
6zvk_1_H2
7a01_1_E2
......@@ -549,15 +448,9 @@
6xzb_1_G2
6gz5_1_BW
6gz3_1_BW
1qzb_1_B
1qza_1_B
1ls2_1_B
3ep2_1_Y
3eq3_1_Y
4v48_1_A6
2z9q_1_A
4hot_1_X
6d2z_1_C
7eh0_1_I
4tu0_1_F
4tu0_1_G
6r9o_1_B
......@@ -572,37 +465,38 @@
6sv4_1_MB
7nrd_1_SM
6i7o_1_MB
1gsg_1_T
6zvi_1_D
6sv4_1_NB
6sv4_1_NC
6i7o_1_NB
1ml5_1_A
7nsq_1_V
7nsp_1_V
6swa_1_Q
6swa_1_R
3j6x_1_IR
3j6y_1_IR
6ole_1_T
6om0_1_T
6oli_1_T
6om7_1_T
6olf_1_T
6w6l_1_T
6tnu_1_M
5mc6_1_M
7nrc_1_SM
6tb3_1_N
7b7d_1_SM
7b7d_1_SN
6tnu_1_N
7nrc_1_SN
7nrd_1_SN
6zot_1_C
4qu6_1_B
2uxb_1_X
2x1f_1_B
2x1a_1_B
3ep2_1_D
3eq3_1_D
1eg0_1_M
3eq4_1_D
5o1y_1_B
3jcr_1_H
4kzy_1_I
4kzz_1_I
4kzx_1_I
6dzi_1_H
5zeu_1_A
6evj_1_N
......@@ -705,7 +599,6 @@
6ip6_1_ZZ
6uu3_1_333
6uu1_1_333
1pn8_1_D
3er8_1_H
3er8_1_G
3er8_1_F
......@@ -744,9 +637,8 @@
4wtl_1_T
4wtl_1_P
1xnq_1_W
1x18_1_C
1x18_1_B
1x18_1_D
7n2v_1_DT
4peh_1_Z
1vq6_1_4
4am3_1_D
4am3_1_H
......@@ -764,6 +656,38 @@
3rtj_1_D
6ty9_1_M
6tz1_1_N
6q1h_1_D
6q1h_1_H
6p7p_1_F
6p7p_1_E
6p7p_1_D
6vm6_1_J
6vm6_1_G
6wan_1_K
6wan_1_H
6wan_1_G
6wan_1_L
6wan_1_I
6ywo_1_F
6wan_1_J
4oau_1_A
6ywo_1_E
6ywo_1_K
6vm6_1_I
6vm6_1_H
6ywo_1_I
2a1r_1_C
6m6v_1_F
6m6v_1_E
2a1r_1_D
3gpq_1_E
3gpq_1_F
6o79_1_C
6vm6_1_K
6m6v_1_G
6hyu_1_D
1laj_1_R
6ybv_1_K
6sce_1_B
6xl1_1_C
6scf_1_I
......@@ -809,31 +733,20 @@
1y1y_1_P
5zuu_1_I
5zuu_1_G
7am2_1_R1
4peh_1_W
4peh_1_V
4peh_1_X
4peh_1_Y
4peh_1_Z
7d8c_1_C
6mkn_1_W
7kl3_1_B
4cxg_1_C
4cxh_1_C
1x1l_1_A
1zc8_1_Z
2ob7_1_D
2ob7_1_A
4eya_1_E
4eya_1_F
4eya_1_Q
4eya_1_R
1qzc_1_B
1t1o_1_B
1mvr_1_C
1t1m_1_B
1t1o_1_C
1t1m_1_A
1t1o_1_A
2r1g_1_B
4ht9_1_E
6z1p_1_AB
6z1p_1_AA
......@@ -844,19 +757,14 @@
5uk4_1_W
5uk4_1_U
5f6c_1_E
7nwh_1_HH
4rcj_1_B
1xnr_1_W
2agn_1_A
2agn_1_C
2agn_1_B
6e0o_1_C
6o75_1_D
6o75_1_C
6e0o_1_B
3j06_1_R
1r2x_1_C
1r2w_1_C
1eg0_1_L
4eya_1_G
4eya_1_H
4eya_1_S
......@@ -866,8 +774,7 @@
1ibm_1_Z
4dr5_1_V
4d61_1_J
1trj_1_B
1trj_1_C
7nwg_1_Q3
5tbw_1_SR
6hhq_1_SR
6zvi_1_H
......@@ -909,14 +816,8 @@
6ppn_1_I
5flx_1_Z
6eri_1_AX
7k5l_1_R
7d80_1_Y
1zc8_1_A
1zc8_1_C
1zc8_1_B
1zc8_1_G
1zc8_1_I
1zc8_1_H
1zc8_1_J
7du2_1_R
4v8z_1_CX
6kqe_1_I
......@@ -930,7 +831,6 @@
4xlr_1_Q
6sty_1_C
6sty_1_F
2xs5_1_D
3ok4_1_N
3ok4_1_L
3ok4_1_Z
......@@ -973,19 +873,17 @@
3ol7_1_H
3ol8_1_L
3ol8_1_P
1qzc_1_C
1qzc_1_A
6yrq_1_E
6yrq_1_H
6yrq_1_G
6yrq_1_F
6yrb_1_C
6yrb_1_D
1mvr_1_D
6gz5_1_BV
6gz4_1_BV
6gz3_1_BV
6fti_1_Q
7njc_1_B
4v7e_1_AB
4v7e_1_AE
4v7e_1_AD
......@@ -997,9 +895,7 @@
3t1h_1_W
3t1y_1_W
1xmo_1_W
4adx_1_9
6kr6_1_B
1zn1_1_B
6z8k_1_X
4csf_1_U
4csf_1_Q
......@@ -1025,7 +921,6 @@
2xpj_1_D
2vrt_1_H
2vrt_1_G
1emi_1_B
6r9m_1_B
4nia_1_C
4nia_1_A
......@@ -1051,45 +946,23 @@
1uvn_1_F
1uvn_1_B
1uvn_1_D
3iy9_1_A
4wtk_1_T
4wtk_1_P
1vqn_1_4
4oav_1_C
4oav_1_A
3ep2_1_E
3eq3_1_E
3eq4_1_E
3ep2_1_A
3eq3_1_A
3eq4_1_A
3ep2_1_C
3eq3_1_C
3eq4_1_C
3ep2_1_B
3eq3_1_B
3eq4_1_B
4i67_1_B
3pgw_1_R
3pgw_1_N
3cw1_1_X
3cw1_1_W
3cw1_1_V
7b0y_1_A
6k32_1_T
6k32_1_P
5mmj_1_A
5x8r_1_A
2agn_1_E
2agn_1_D
4v5z_1_BD
6yw5_1_AA
6ywe_1_AA
6ywy_1_AA
6ywx_1_AA
3nvk_1_G
3nvk_1_S
2iy3_1_B
1cwp_1_D
1cwp_1_F
5z4j_1_B
5gmf_1_E
......@@ -1129,7 +1002,6 @@
4kzz_1_J
7a09_1_F
5t2c_1_AN
4v5z_1_BF
3j6b_1_E
4v4f_1_B6
4v4f_1_A5
......@@ -1153,21 +1025,21 @@
4v4f_1_B4
4v4f_1_A6
4v4f_1_B2
7m4y_1_V
7m4x_1_V
6v3a_1_V
6v39_1_V
5it9_1_I
7jqc_1_I
5zsb_1_C
5zsb_1_D
5zsn_1_D
5zsn_1_E
1cwp_1_D
3jcr_1_N
6gfw_1_R
2vaz_1_A
6zm6_1_X
6zm5_1_X
6zm6_1_W
6zm5_1_W
4v5z_1_BP
6n6e_1_D
4g7o_1_I
4g7o_1_S
......@@ -1177,11 +1049,9 @@
5uh6_1_I
6l74_1_I
5uh9_1_I
2ftc_1_R
7a5j_1_X
6sag_1_R
4udv_1_R
2r1g_1_E
5zsc_1_D
5zsc_1_C
6woy_1_I
......@@ -1209,7 +1079,6 @@
3m85_1_X
3m85_1_Z
3m85_1_Y
1e8s_1_C
5wnp_1_B
5wnv_1_B
5yts_1_B
......@@ -1232,8 +1101,11 @@
6ij2_1_E
3u2e_1_D
3u2e_1_C
7eh1_1_I
5uef_1_C
5uef_1_D
7eh2_1_R
7eh2_1_I
4x4u_1_H
4afy_1_D
6oy5_1_I
......@@ -1249,8 +1121,6 @@
4k4s_1_H
4k4t_1_H
4k4t_1_D
1zn1_1_C
1zn0_1_C
1xpu_1_G
1xpu_1_L
1xpr_1_L
......@@ -1275,6 +1145,7 @@
6gc5_1_H
6gc5_1_G
1n1h_1_B
7n2v_1_PT
4ohz_1_B
6t83_1_6B
4gv6_1_C
......@@ -1287,14 +1158,11 @@
6qx3_1_G
2xnr_1_C
4gkj_1_W
4v5z_1_BC
5y88_1_X
4v5z_1_BB
3j0o_1_H
3j0l_1_H
3j0p_1_H
3j0q_1_H
4v5z_1_BH
3j0o_1_F
3j0l_1_F
3j0p_1_F
......@@ -1309,7 +1177,6 @@
3j0l_1_A
3j0q_1_A
3j0p_1_A
4v5z_1_BJ
6ys3_1_V
6qdw_1_V
5hk0_1_F
......@@ -1345,14 +1212,10 @@
5mrc_1_BB
5mre_1_BB
5mrf_1_BB
4v5z_1_BN
3j46_1_P
3jcr_1_M
4e6b_1_A
4e6b_1_B
6a6l_1_D
4v5z_1_BS
4v8t_1_1
1uvi_1_D
1uvi_1_F
1uvi_1_E
......@@ -1376,10 +1239,7 @@
6ip5_1_2M
6ip6_1_2M
6qcs_1_M
486d_1_G
2r1g_1_C
486d_1_F
4v5z_1_B0
7b5k_1_Z
4nia_1_O
4nia_1_J
4nia_1_K
......@@ -1391,13 +1251,11 @@
4oq9_1_F
4oq9_1_L
6r9q_1_B
7m4u_1_A
6v3a_1_SN1
6v3b_1_SN1
6v39_1_SN1
6v3e_1_SN1
1pn7_1_C
1mj1_1_Q
1mj1_1_R
4dr6_1_V
6kql_1_I
4eya_1_M
......@@ -1437,13 +1295,20 @@
6ow3_1_I
6ovy_1_I
6oy6_1_I
4bbl_1_Y
4bbl_1_Z
4qvd_1_H
5gxi_1_B
3iy8_1_A
6tnu_1_M
5mc6_1_M
7n06_1_G
7n06_1_H
7n06_1_I
7n06_1_J
7n06_1_K
7n06_1_L
7n33_1_G
7n33_1_H
7n33_1_I
7n33_1_J
7n33_1_K
7n33_1_L
5mc6_1_N
4eya_1_O
4eya_1_P
......@@ -1453,33 +1318,13 @@
6htq_1_W
6htq_1_U
6uu6_1_333
6v3a_1_V
6v39_1_V
5a0v_1_F
3avt_1_T
6d1v_1_C
4s2x_1_B
4s2y_1_B
5wnu_1_B
1zc8_1_F
1vtm_1_R
4v5z_1_BA
4v5z_1_BE
4v5z_1_BG
4v5z_1_BI
4v5z_1_BK
4v5z_1_BM
4v5z_1_BL
4v5z_1_BV
4v5z_1_BO
4v5z_1_BQ
4v5z_1_BR
4v5z_1_BT
4v5z_1_BU
4v5z_1_BW
4v5z_1_BY
4v5z_1_BX
4v5z_1_BZ
5elt_1_F
5elt_1_E
6xlj_1_R
......@@ -1492,11 +1337,11 @@
6bk8_1_I
4cxg_1_B
4cxh_1_B
4v5z_1_B1
5z4d_1_B
6o78_1_E
6xa1_1_BV
6ha8_1_X
2xs5_1_D
1m8w_1_E
1m8w_1_F
5udi_1_B
......@@ -1525,11 +1370,13 @@
3rzo_1_R
2f4v_1_Z
1qln_1_R
3cw1_1_X
3cw1_1_W
7b0y_1_A
6ogy_1_M
6ogy_1_N
6uej_1_B
6ywy_1_BB
1x18_1_A
5ytx_1_B
4g0a_1_H
6r9p_1_B
......@@ -1559,11 +1406,6 @@
5lzc_1_W
5lzb_1_W
3wzi_1_C
1mvr_1_E
1mvr_1_B
1mvr_1_A
4adx_1_0
4adx_1_8
1n33_1_Z
6dti_1_W
3d2s_1_F
......@@ -1572,12 +1414,7 @@
5mre_1_AA
5mrf_1_AA
7jhy_1_Z
2r1g_1_A
2r1g_1_D
2r1g_1_F
3eq4_1_Y
4wkr_1_C
2r1g_1_X
4v99_1_EC
4v99_1_AC
4v99_1_BH
......@@ -1647,38 +1484,6 @@
2xs7_1_B
1n38_1_B
4qvc_1_G
6q1h_1_D
6q1h_1_H
6p7p_1_F
6p7p_1_E
6p7p_1_D
6vm6_1_J
6vm6_1_G
6wan_1_K
6wan_1_H
6wan_1_G
6wan_1_L
6wan_1_I
6ywo_1_F
6wan_1_J
4oau_1_A
6ywo_1_E
6ywo_1_K
6vm6_1_I
6vm6_1_H
6ywo_1_I
2a1r_1_C
6m6v_1_F
6m6v_1_E
2a1r_1_D
3gpq_1_E
3gpq_1_F
6o79_1_C
6vm6_1_K
6m6v_1_G
6hyu_1_D
1laj_1_R
6ybv_1_K
6mpf_1_W
6spc_1_A
6spe_1_A
......@@ -1692,43 +1497,36 @@
4g0a_1_E
2b2d_1_S
5hkc_1_C
4kzy_1_I
4kzz_1_I
4kzx_1_I
1rmv_1_B
4qu7_1_X
4qu7_1_V
4qu7_1_U
4v5z_1_AH
4v5z_1_AA
4v5z_1_AB
4v5z_1_AC
4v5z_1_AD
4v5z_1_AE
4v5z_1_AF
4v5z_1_AG
6pmi_1_3
6pmj_1_3
5hjz_1_C
7nrc_1_SM
7nrc_1_SN
7am2_1_R1
7k5l_1_R
7b5k_1_X
7d8c_1_C
7m4y_1_V
7m4x_1_V
7b5k_1_Z
7m4u_1_A
7n06_1_G
7n06_1_H
7n06_1_I
7n06_1_J
7n06_1_K
7n06_1_L
7n33_1_G
7n33_1_H
7n33_1_I
7n33_1_J
7n33_1_K
7n33_1_L
6ydp_1_AA_1176-2737
6ydw_1_AA_1176-2737
1vy7_1_AY_1-73
1vy7_1_CY_1-73
4w2h_1_CY_1-73
7d1a_1_A_805-902
7d0g_1_A_805-913
7d0f_1_A_817-913
7o7z_1_AH_144-220
4c9d_1_D_29-1
4c9d_1_C_29-1
7aih_1_1_2400-2963
7aih_1_1_2984-3610
7ane_1_2_1904-2468
7ane_1_2_2489-3115
5g2x_1_A_595-692
7aor_1_2_2020-2579
7aor_1_2_2589-3210
7a5p_1_2_259-449
7aor_1_A_2020-2579
7aor_1_A_2589-3210
7am2_1_1_1904-2470
7am2_1_1_2491-3117
7ane_1_1_1904-2468
7ane_1_1_2489-3115
6uz7_1_8_2140-2825
......
6ydp_1_AA_1176-2737
Could not find nucleotides of chain AA in annotation 6ydp.json. Either there is a problem with 6ydp mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
6ydw_1_AA_1176-2737
Could not find nucleotides of chain AA in annotation 6ydw.json. Either there is a problem with 6ydw mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
2z9q_1_A_1-72
DSSR warning 2z9q.json: no nucleotides found. Ignoring 2z9q_1_A_1-72.
1ml5_1_b_5-121
Could not find nucleotides of chain b in annotation 1ml5.json. Either there is a problem with 1ml5 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
1ml5_1_a_1-2914
Could not find nucleotides of chain a in annotation 1ml5.json. Either there is a problem with 1ml5 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
3ep2_1_Y_1-72
DSSR warning 3ep2.json: no nucleotides found. Ignoring 3ep2_1_Y_1-72.
3eq3_1_Y_1-72
DSSR warning 3eq3.json: no nucleotides found. Ignoring 3eq3_1_Y_1-72.
4v48_1_A6_1-73
DSSR warning 4v48.json: no nucleotides found. Ignoring 4v48_1_A6_1-73.
1ml5_1_A_2-1520
Could not find nucleotides of chain A in annotation 1ml5.json. Either there is a problem with 1ml5 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
1qzb_1_B_1-73
DSSR warning 1qzb.json: no nucleotides found. Ignoring 1qzb_1_B_1-73.
1qza_1_B_1-73
DSSR warning 1qza.json: no nucleotides found. Ignoring 1qza_1_B_1-73.
1ls2_1_B_1-73
DSSR warning 1ls2.json: no nucleotides found. Ignoring 1ls2_1_B_1-73.
1gsg_1_T_1-72
DSSR warning 1gsg.json: no nucleotides found. Ignoring 1gsg_1_T_1-72.
7d1a_1_A_805-902
Could not find nucleotides of chain A in annotation 7d1a.json. Either there is a problem with 7d1a mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7d0g_1_A_805-913
Could not find nucleotides of chain A in annotation 7d0g.json. Either there is a problem with 7d0g mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7d0f_1_A_817-913
Could not find nucleotides of chain A in annotation 7d0f.json. Either there is a problem with 7d0f mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
3jcr_1_H_1-115
DSSR warning 3jcr.json: no nucleotides found. Ignoring 3jcr_1_H_1-115.
1vy7_1_AY_1-73
Sequence is too short. (< 5 resolved nts)
1vy7_1_CY_1-73
Sequence is too short. (< 5 resolved nts)
4w2h_1_CY_1-73
Sequence is too short. (< 5 resolved nts)
5zzm_1_M_3-118
DSSR warning 5zzm.json: no nucleotides found. Ignoring 5zzm_1_M_3-118.
2rdo_1_A_3-118
DSSR warning 2rdo.json: no nucleotides found. Ignoring 2rdo_1_A_3-118.
4v48_1_A9_3-118
DSSR warning 4v48.json: no nucleotides found. Ignoring 4v48_1_A9_3-118.
4v47_1_A9_3-118
DSSR warning 4v47.json: no nucleotides found. Ignoring 4v47_1_A9_3-118.
2ob7_1_A_10-319
DSSR warning 2ob7.json: no nucleotides found. Ignoring 2ob7_1_A_10-319.
1x1l_1_A_1-130
DSSR warning 1x1l.json: no nucleotides found. Ignoring 1x1l_1_A_1-130.
1zc8_1_Z_1-91
DSSR warning 1zc8.json: no nucleotides found. Ignoring 1zc8_1_Z_1-91.
2ob7_1_D_1-130
DSSR warning 2ob7.json: no nucleotides found. Ignoring 2ob7_1_D_1-130.
4v42_1_BA_1-2914
Could not find nucleotides of chain BA in annotation 4v42.json. Either there is a problem with 4v42 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
4v42_1_BB_5-121
Could not find nucleotides of chain BB in annotation 4v42.json. Either there is a problem with 4v42 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
1r2x_1_C_1-58
DSSR warning 1r2x.json: no nucleotides found. Ignoring 1r2x_1_C_1-58.
1r2w_1_C_1-58
DSSR warning 1r2w.json: no nucleotides found. Ignoring 1r2w_1_C_1-58.
1eg0_1_L_1-56
DSSR warning 1eg0.json: no nucleotides found. Ignoring 1eg0_1_L_1-56.
3dg2_1_A_1-1542
DSSR warning 3dg2.json: no nucleotides found. Ignoring 3dg2_1_A_1-1542.
3dg0_1_A_1-1542
DSSR warning 3dg0.json: no nucleotides found. Ignoring 3dg0_1_A_1-1542.
4v48_1_BA_1-1543
DSSR warning 4v48.json: no nucleotides found. Ignoring 4v48_1_BA_1-1543.
4v47_1_BA_1-1542
DSSR warning 4v47.json: no nucleotides found. Ignoring 4v47_1_BA_1-1542.
3dg4_1_A_1-1542
DSSR warning 3dg4.json: no nucleotides found. Ignoring 3dg4_1_A_1-1542.
3dg5_1_A_1-1542
DSSR warning 3dg5.json: no nucleotides found. Ignoring 3dg5_1_A_1-1542.
5zzm_1_N_1-2903
DSSR warning 5zzm.json: no nucleotides found. Ignoring 5zzm_1_N_1-2903.
2rdo_1_B_1-2904
DSSR warning 2rdo.json: no nucleotides found. Ignoring 2rdo_1_B_1-2904.
3dg2_1_B_1-2904
DSSR warning 3dg2.json: no nucleotides found. Ignoring 3dg2_1_B_1-2904.
3dg0_1_B_1-2904
DSSR warning 3dg0.json: no nucleotides found. Ignoring 3dg0_1_B_1-2904.
4v48_1_A0_1-2904
DSSR warning 4v48.json: no nucleotides found. Ignoring 4v48_1_A0_1-2904.
4v47_1_A0_1-2904
DSSR warning 4v47.json: no nucleotides found. Ignoring 4v47_1_A0_1-2904.
3dg4_1_B_1-2904
DSSR warning 3dg4.json: no nucleotides found. Ignoring 3dg4_1_B_1-2904.
3dg5_1_B_1-2904
DSSR warning 3dg5.json: no nucleotides found. Ignoring 3dg5_1_B_1-2904.
1eg0_1_O_1-73
DSSR warning 1eg0.json: no nucleotides found. Ignoring 1eg0_1_O_1-73.
1zc8_1_A_1-59
DSSR warning 1zc8.json: no nucleotides found. Ignoring 1zc8_1_A_1-59.
1jgq_1_A_2-1520
Could not find nucleotides of chain A in annotation 1jgq.json. Either there is a problem with 1jgq mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
4v42_1_AA_2-1520
Could not find nucleotides of chain AA in annotation 4v42.json. Either there is a problem with 4v42 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
1jgo_1_A_2-1520
Could not find nucleotides of chain A in annotation 1jgo.json. Either there is a problem with 1jgo mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
1jgp_1_A_2-1520
Could not find nucleotides of chain A in annotation 1jgp.json. Either there is a problem with 1jgp mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
1mvr_1_D_1-59
DSSR warning 1mvr.json: no nucleotides found. Ignoring 1mvr_1_D_1-59.
4c9d_1_D_29-1
Mapping is reversed, this case is not supported (yet).
4c9d_1_C_29-1
Mapping is reversed, this case is not supported (yet).
4adx_1_9_1-121
DSSR warning 4adx.json: no nucleotides found. Ignoring 4adx_1_9_1-121.
1zn1_1_B_1-59
DSSR warning 1zn1.json: no nucleotides found. Ignoring 1zn1_1_B_1-59.
1emi_1_B_1-108
DSSR warning 1emi.json: no nucleotides found. Ignoring 1emi_1_B_1-108.
3iy9_1_A_498-1027
DSSR warning 3iy9.json: no nucleotides found. Ignoring 3iy9_1_A_498-1027.
3ep2_1_B_1-50
DSSR warning 3ep2.json: no nucleotides found. Ignoring 3ep2_1_B_1-50.
3eq3_1_B_1-50
DSSR warning 3eq3.json: no nucleotides found. Ignoring 3eq3_1_B_1-50.
3eq4_1_B_1-50
DSSR warning 3eq4.json: no nucleotides found. Ignoring 3eq4_1_B_1-50.
3pgw_1_R_1-164
DSSR warning 3pgw.json: no nucleotides found. Ignoring 3pgw_1_R_1-164.
3pgw_1_N_1-164
DSSR warning 3pgw.json: no nucleotides found. Ignoring 3pgw_1_N_1-164.
3cw1_1_x_1-138
DSSR warning 3cw1.json: no nucleotides found. Ignoring 3cw1_1_x_1-138.
3cw1_1_w_1-138
DSSR warning 3cw1.json: no nucleotides found. Ignoring 3cw1_1_w_1-138.
3cw1_1_V_1-138
DSSR warning 3cw1.json: no nucleotides found. Ignoring 3cw1_1_V_1-138.
3cw1_1_v_1-138
DSSR warning 3cw1.json: no nucleotides found. Ignoring 3cw1_1_v_1-138.
2iy3_1_B_9-105
DSSR warning 2iy3.json: no nucleotides found. Ignoring 2iy3_1_B_9-105.
3jcr_1_N_1-106
DSSR warning 3jcr.json: no nucleotides found. Ignoring 3jcr_1_N_1-106.
2vaz_1_A_64-177
DSSR warning 2vaz.json: no nucleotides found. Ignoring 2vaz_1_A_64-177.
2ftc_1_R_81-1466
DSSR warning 2ftc.json: no nucleotides found. Ignoring 2ftc_1_R_81-1466.
3jcr_1_M_1-141
DSSR warning 3jcr.json: no nucleotides found. Ignoring 3jcr_1_M_1-141.
4v5z_1_B0_1-2902
DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_B0_1-2902.
5g2x_1_A_595-692
Sequence is too short. (< 5 resolved nts)
3iy8_1_A_1-540
DSSR warning 3iy8.json: no nucleotides found. Ignoring 3iy8_1_A_1-540.
4v5z_1_BY_2-113
DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_BY_2-113.
4v5z_1_BZ_1-70
DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_BZ_1-70.
4v5z_1_B1_2-123
DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_B1_2-123.
1mvr_1_B_1-96
DSSR warning 1mvr.json: no nucleotides found. Ignoring 1mvr_1_B_1-96.
4adx_1_0_1-2923
DSSR warning 4adx.json: no nucleotides found. Ignoring 4adx_1_0_1-2923.
3eq4_1_Y_1-69
DSSR warning 3eq4.json: no nucleotides found. Ignoring 3eq4_1_Y_1-69.
7a5p_1_2_259-449
Could not find nucleotides of chain 2 in annotation 7a5p.json. Either there is a problem with 7a5p mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
6uz7_1_8_2140-2825
Could not find nucleotides of chain 8 in annotation 6uz7.json. Either there is a problem with 6uz7 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
4v5z_1_AA_1-1563
DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_AA_1-1563.
6cfj_1_1X
Could not find nucleotides of chain 1X in annotation 6cfj.json. Either there is a problem with 6cfj mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
......@@ -592,9 +334,6 @@ Could not find nucleotides of chain W in annotation 6h58.json. Either there is a
6h58_1_WW
Could not find nucleotides of chain WW in annotation 6h58.json. Either there is a problem with 6h58 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
1eg0_1_O
DSSR warning 1eg0.json: no nucleotides found. Ignoring 1eg0_1_O.
5j8b_1_X
Could not find nucleotides of chain X in annotation 5j8b.json. Either there is a problem with 5j8b mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
......@@ -676,18 +415,6 @@ Could not find nucleotides of chain A in annotation 6ys3.json. Either there is a
6qdw_1_A
Could not find nucleotides of chain A in annotation 6qdw.json. Either there is a problem with 6qdw mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
5zzm_1_M
DSSR warning 5zzm.json: no nucleotides found. Ignoring 5zzm_1_M.
2rdo_1_A
DSSR warning 2rdo.json: no nucleotides found. Ignoring 2rdo_1_A.
4v48_1_A9
DSSR warning 4v48.json: no nucleotides found. Ignoring 4v48_1_A9.
4v47_1_A9
DSSR warning 4v47.json: no nucleotides found. Ignoring 4v47_1_A9.
6hcj_1_Q3
Could not find nucleotides of chain Q3 in annotation 6hcj.json. Either there is a problem with 6hcj mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
......@@ -889,9 +616,24 @@ Could not find nucleotides of chain X in annotation 4w2e.json. Either there is a
6ucq_1_2X
Could not find nucleotides of chain 2X in annotation 6ucq.json. Either there is a problem with 6ucq mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7n1p_1_DT
Could not find nucleotides of chain DT in annotation 7n1p.json. Either there is a problem with 7n1p mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7n2u_1_DT
Could not find nucleotides of chain DT in annotation 7n2u.json. Either there is a problem with 7n2u mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
6yss_1_W
Could not find nucleotides of chain W in annotation 6yss.json. Either there is a problem with 6yss mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7n30_1_DT
Could not find nucleotides of chain DT in annotation 7n30.json. Either there is a problem with 7n30 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7n31_1_DT
Could not find nucleotides of chain DT in annotation 7n31.json. Either there is a problem with 7n31 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7n2c_1_DT
Could not find nucleotides of chain DT in annotation 7n2c.json. Either there is a problem with 7n2c mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
5afi_1_Y
Could not find nucleotides of chain Y in annotation 5afi.json. Either there is a problem with 5afi mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
......@@ -967,27 +709,12 @@ Could not find nucleotides of chain X in annotation 5uq8.json. Either there is a
5uq7_1_X
Could not find nucleotides of chain X in annotation 5uq7.json. Either there is a problem with 5uq7 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
1jgq_1_A
Could not find nucleotides of chain A in annotation 1jgq.json. Either there is a problem with 1jgq mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
4v42_1_AA
Could not find nucleotides of chain AA in annotation 4v42.json. Either there is a problem with 4v42 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
1jgo_1_A
Could not find nucleotides of chain A in annotation 1jgo.json. Either there is a problem with 1jgo mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
1jgp_1_A
Could not find nucleotides of chain A in annotation 1jgp.json. Either there is a problem with 1jgp mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
4v4j_1_W
Could not find nucleotides of chain W in annotation 4v4j.json. Either there is a problem with 4v4j mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
4v4i_1_W
Could not find nucleotides of chain W in annotation 4v4i.json. Either there is a problem with 4v4i mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
4v42_1_BA
Could not find nucleotides of chain BA in annotation 4v42.json. Either there is a problem with 4v42 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
4wt8_1_CS
Could not find nucleotides of chain CS in annotation 4wt8.json. Either there is a problem with 4wt8 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
......@@ -1000,8 +727,29 @@ Could not find nucleotides of chain X in annotation 4v4j.json. Either there is a
4v4i_1_X
Could not find nucleotides of chain X in annotation 4v4i.json. Either there is a problem with 4v4i mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
4v42_1_BB
Could not find nucleotides of chain BB in annotation 4v42.json. Either there is a problem with 4v42 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
6lkq_1_S
Could not find nucleotides of chain S in annotation 6lkq.json. Either there is a problem with 6lkq mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
5h5u_1_H
Could not find nucleotides of chain H in annotation 5h5u.json. Either there is a problem with 5h5u mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7d6z_1_F
Could not find nucleotides of chain F in annotation 7d6z.json. Either there is a problem with 7d6z mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
5lze_1_Y
Could not find nucleotides of chain Y in annotation 5lze.json. Either there is a problem with 5lze mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
5lze_1_V
Could not find nucleotides of chain V in annotation 5lze.json. Either there is a problem with 5lze mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
5lze_1_X
Could not find nucleotides of chain X in annotation 5lze.json. Either there is a problem with 5lze mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
3jcj_1_G
Could not find nucleotides of chain G in annotation 3jcj.json. Either there is a problem with 3jcj mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
6o7k_1_G
Could not find nucleotides of chain G in annotation 6o7k.json. Either there is a problem with 6o7k mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
6d30_1_C
Sequence is too short. (< 5 resolved nts)
......@@ -1105,9 +853,6 @@ Sequence is too short. (< 5 resolved nts)
6rt5_1_E
Sequence is too short. (< 5 resolved nts)
4qu6_1_B
Sequence is too short. (< 5 resolved nts)
6lkq_1_T
Could not find nucleotides of chain T in annotation 6lkq.json. Either there is a problem with 6lkq mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
......@@ -1123,30 +868,6 @@ Could not find nucleotides of chain B in annotation 3jbv.json. Either there is a
3jbu_1_B
Could not find nucleotides of chain B in annotation 3jbu.json. Either there is a problem with 3jbu mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
5zzm_1_N
DSSR warning 5zzm.json: no nucleotides found. Ignoring 5zzm_1_N.
2rdo_1_B
DSSR warning 2rdo.json: no nucleotides found. Ignoring 2rdo_1_B.
3dg2_1_B
DSSR warning 3dg2.json: no nucleotides found. Ignoring 3dg2_1_B.
3dg0_1_B
DSSR warning 3dg0.json: no nucleotides found. Ignoring 3dg0_1_B.
4v48_1_A0
DSSR warning 4v48.json: no nucleotides found. Ignoring 4v48_1_A0.
4v47_1_A0
DSSR warning 4v47.json: no nucleotides found. Ignoring 4v47_1_A0.
3dg4_1_B
DSSR warning 3dg4.json: no nucleotides found. Ignoring 3dg4_1_B.
3dg5_1_B
DSSR warning 3dg5.json: no nucleotides found. Ignoring 3dg5_1_B.
6do8_1_B
Sequence is too short. (< 5 resolved nts)
......@@ -1315,48 +1036,6 @@ Sequence is too short. (< 5 resolved nts)
6n6g_1_D
Sequence is too short. (< 5 resolved nts)
6lkq_1_S
Could not find nucleotides of chain S in annotation 6lkq.json. Either there is a problem with 6lkq mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
5h5u_1_H
Could not find nucleotides of chain H in annotation 5h5u.json. Either there is a problem with 5h5u mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7d6z_1_F
Could not find nucleotides of chain F in annotation 7d6z.json. Either there is a problem with 7d6z mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
5lze_1_Y
Could not find nucleotides of chain Y in annotation 5lze.json. Either there is a problem with 5lze mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
5lze_1_V
Could not find nucleotides of chain V in annotation 5lze.json. Either there is a problem with 5lze mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
5lze_1_X
Could not find nucleotides of chain X in annotation 5lze.json. Either there is a problem with 5lze mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
3jcj_1_G
Could not find nucleotides of chain G in annotation 3jcj.json. Either there is a problem with 3jcj mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
6o7k_1_G
Could not find nucleotides of chain G in annotation 6o7k.json. Either there is a problem with 6o7k mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
3dg2_1_A
DSSR warning 3dg2.json: no nucleotides found. Ignoring 3dg2_1_A.
3dg0_1_A
DSSR warning 3dg0.json: no nucleotides found. Ignoring 3dg0_1_A.
4v48_1_BA
DSSR warning 4v48.json: no nucleotides found. Ignoring 4v48_1_BA.
4v47_1_BA
DSSR warning 4v47.json: no nucleotides found. Ignoring 4v47_1_BA.
3dg4_1_A
DSSR warning 3dg4.json: no nucleotides found. Ignoring 3dg4_1_A.
3dg5_1_A
DSSR warning 3dg5.json: no nucleotides found. Ignoring 3dg5_1_A.
4b3r_1_W
Sequence is too short. (< 5 resolved nts)
......@@ -1366,12 +1045,30 @@ Sequence is too short. (< 5 resolved nts)
4b3s_1_W
Sequence is too short. (< 5 resolved nts)
7b5k_1_X
Could not find nucleotides of chain X in annotation 7b5k.json. Either there is a problem with 7b5k mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
5o2r_1_X
Could not find nucleotides of chain X in annotation 5o2r.json. Either there is a problem with 5o2r mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
5kcs_1_1X
Could not find nucleotides of chain 1X in annotation 5kcs.json. Either there is a problem with 5kcs mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7n1p_1_PT
Could not find nucleotides of chain PT in annotation 7n1p.json. Either there is a problem with 7n1p mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7n2u_1_PT
Could not find nucleotides of chain PT in annotation 7n2u.json. Either there is a problem with 7n2u mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7n30_1_PT
Could not find nucleotides of chain PT in annotation 7n30.json. Either there is a problem with 7n30 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7n31_1_PT
Could not find nucleotides of chain PT in annotation 7n31.json. Either there is a problem with 7n31 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7n2c_1_PT
Could not find nucleotides of chain PT in annotation 7n2c.json. Either there is a problem with 7n2c mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
6zvk_1_E2
Could not find nucleotides of chain E2 in annotation 6zvk.json. Either there is a problem with 6zvk mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
......@@ -1651,33 +1348,15 @@ Could not find nucleotides of chain BW in annotation 6gz5.json. Either there is
6gz3_1_BW
Could not find nucleotides of chain BW in annotation 6gz3.json. Either there is a problem with 6gz3 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
1qzb_1_B
DSSR warning 1qzb.json: no nucleotides found. Ignoring 1qzb_1_B.
1qza_1_B
DSSR warning 1qza.json: no nucleotides found. Ignoring 1qza_1_B.
1ls2_1_B
DSSR warning 1ls2.json: no nucleotides found. Ignoring 1ls2_1_B.
3ep2_1_Y
DSSR warning 3ep2.json: no nucleotides found. Ignoring 3ep2_1_Y.
3eq3_1_Y
DSSR warning 3eq3.json: no nucleotides found. Ignoring 3eq3_1_Y.
4v48_1_A6
DSSR warning 4v48.json: no nucleotides found. Ignoring 4v48_1_A6.
2z9q_1_A
DSSR warning 2z9q.json: no nucleotides found. Ignoring 2z9q_1_A.
4hot_1_X
Sequence is too short. (< 5 resolved nts)
6d2z_1_C
Sequence is too short. (< 5 resolved nts)
7eh0_1_I
Sequence is too short. (< 5 resolved nts)
4tu0_1_F
Sequence is too short. (< 5 resolved nts)
......@@ -1720,9 +1399,6 @@ Could not find nucleotides of chain SM in annotation 7nrd.json. Either there is
6i7o_1_MB
Could not find nucleotides of chain MB in annotation 6i7o.json. Either there is a problem with 6i7o mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
1gsg_1_T
DSSR warning 1gsg.json: no nucleotides found. Ignoring 1gsg_1_T.
6zvi_1_D
Could not find nucleotides of chain D in annotation 6zvi.json. Either there is a problem with 6zvi mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
......@@ -1735,8 +1411,11 @@ Could not find nucleotides of chain NC in annotation 6sv4.json. Either there is
6i7o_1_NB
Could not find nucleotides of chain NB in annotation 6i7o.json. Either there is a problem with 6i7o mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
1ml5_1_A
Could not find nucleotides of chain A in annotation 1ml5.json. Either there is a problem with 1ml5 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7nsq_1_V
Could not find nucleotides of chain V in annotation 7nsq.json. Either there is a problem with 7nsq mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7nsp_1_V
Could not find nucleotides of chain V in annotation 7nsp.json. Either there is a problem with 7nsp mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
6swa_1_Q
Could not find nucleotides of chain Q in annotation 6swa.json. Either there is a problem with 6swa mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
......@@ -1744,12 +1423,6 @@ Could not find nucleotides of chain Q in annotation 6swa.json. Either there is a
6swa_1_R
Could not find nucleotides of chain R in annotation 6swa.json. Either there is a problem with 6swa mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
3j6x_1_IR
Could not find nucleotides of chain IR in annotation 3j6x.json. Either there is a problem with 3j6x mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
3j6y_1_IR
Could not find nucleotides of chain IR in annotation 3j6y.json. Either there is a problem with 3j6y mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
6ole_1_T
Could not find nucleotides of chain T in annotation 6ole.json. Either there is a problem with 6ole mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
......@@ -1768,6 +1441,15 @@ Could not find nucleotides of chain T in annotation 6olf.json. Either there is a
6w6l_1_T
Could not find nucleotides of chain T in annotation 6w6l.json. Either there is a problem with 6w6l mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
6tnu_1_M
Could not find nucleotides of chain M in annotation 6tnu.json. Either there is a problem with 6tnu mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
5mc6_1_M
Could not find nucleotides of chain M in annotation 5mc6.json. Either there is a problem with 5mc6 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7nrc_1_SM
Could not find nucleotides of chain SM in annotation 7nrc.json. Either there is a problem with 7nrc mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
6tb3_1_N
Could not find nucleotides of chain N in annotation 6tb3.json. Either there is a problem with 6tb3 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
......@@ -1780,12 +1462,18 @@ Could not find nucleotides of chain SN in annotation 7b7d.json. Either there is
6tnu_1_N
Could not find nucleotides of chain N in annotation 6tnu.json. Either there is a problem with 6tnu mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7nrc_1_SN
Could not find nucleotides of chain SN in annotation 7nrc.json. Either there is a problem with 7nrc mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7nrd_1_SN
Could not find nucleotides of chain SN in annotation 7nrd.json. Either there is a problem with 7nrd mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
6zot_1_C
Sequence is too short. (< 5 resolved nts)
4qu6_1_B
Sequence is too short. (< 5 resolved nts)
2uxb_1_X
Sequence is too short. (< 5 resolved nts)
......@@ -1795,23 +1483,17 @@ Sequence is too short. (< 5 resolved nts)
2x1a_1_B
Sequence is too short. (< 5 resolved nts)
3ep2_1_D
DSSR warning 3ep2.json: no nucleotides found. Ignoring 3ep2_1_D.
3eq3_1_D
DSSR warning 3eq3.json: no nucleotides found. Ignoring 3eq3_1_D.
1eg0_1_M
DSSR warning 1eg0.json: no nucleotides found. Ignoring 1eg0_1_M.
3eq4_1_D
DSSR warning 3eq4.json: no nucleotides found. Ignoring 3eq4_1_D.
5o1y_1_B
Sequence is too short. (< 5 resolved nts)
3jcr_1_H
DSSR warning 3jcr.json: no nucleotides found. Ignoring 3jcr_1_H.
4kzy_1_I
Could not find nucleotides of chain I in annotation 4kzy.json. Either there is a problem with 4kzy mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
4kzz_1_I
Could not find nucleotides of chain I in annotation 4kzz.json. Either there is a problem with 4kzz mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
4kzx_1_I
Could not find nucleotides of chain I in annotation 4kzx.json. Either there is a problem with 4kzx mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
6dzi_1_H
Could not find nucleotides of chain H in annotation 6dzi.json. Either there is a problem with 6dzi mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
......@@ -2119,9 +1801,6 @@ Sequence is too short. (< 5 resolved nts)
6uu1_1_333
Sequence is too short. (< 5 resolved nts)
1pn8_1_D
DSSR warning 1pn8.json: no nucleotides found. Ignoring 1pn8_1_D.
3er8_1_H
Sequence is too short. (< 5 resolved nts)
......@@ -2180,7 +1859,7 @@ Sequence is too short. (< 5 resolved nts)
Sequence is too short. (< 5 resolved nts)
1mvr_1_1
DSSR warning 1mvr.json: no nucleotides found. Ignoring 1mvr_1_1.
Sequence is too short. (< 5 resolved nts)
6vyt_1_Y
Sequence is too short. (< 5 resolved nts)
......@@ -2236,14 +1915,11 @@ Sequence is too short. (< 5 resolved nts)
1xnq_1_W
Sequence is too short. (< 5 resolved nts)
1x18_1_C
DSSR warning 1x18.json: no nucleotides found. Ignoring 1x18_1_C.
1x18_1_B
DSSR warning 1x18.json: no nucleotides found. Ignoring 1x18_1_B.
7n2v_1_DT
Could not find nucleotides of chain DT in annotation 7n2v.json. Either there is a problem with 7n2v mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
1x18_1_D
DSSR warning 1x18.json: no nucleotides found. Ignoring 1x18_1_D.
4peh_1_Z
Sequence is too short. (< 5 resolved nts)
1vq6_1_4
Sequence is too short. (< 5 resolved nts)
......@@ -2296,22 +1972,118 @@ Sequence is too short. (< 5 resolved nts)
6tz1_1_N
Sequence is too short. (< 5 resolved nts)
6sce_1_B
6q1h_1_D
Sequence is too short. (< 5 resolved nts)
6xl1_1_C
6q1h_1_H
Sequence is too short. (< 5 resolved nts)
6scf_1_I
6p7p_1_F
Sequence is too short. (< 5 resolved nts)
6scf_1_K
6p7p_1_E
Sequence is too short. (< 5 resolved nts)
6yud_1_K
6p7p_1_D
Sequence is too short. (< 5 resolved nts)
6yud_1_O
6vm6_1_J
Sequence is too short. (< 5 resolved nts)
6vm6_1_G
Sequence is too short. (< 5 resolved nts)
6wan_1_K
Sequence is too short. (< 5 resolved nts)
6wan_1_H
Sequence is too short. (< 5 resolved nts)
6wan_1_G
Sequence is too short. (< 5 resolved nts)
6wan_1_L
Sequence is too short. (< 5 resolved nts)
6wan_1_I
Sequence is too short. (< 5 resolved nts)
6ywo_1_F
Sequence is too short. (< 5 resolved nts)
6wan_1_J
Sequence is too short. (< 5 resolved nts)
4oau_1_A
Sequence is too short. (< 5 resolved nts)
6ywo_1_E
Sequence is too short. (< 5 resolved nts)
6ywo_1_K
Sequence is too short. (< 5 resolved nts)
6vm6_1_I
Sequence is too short. (< 5 resolved nts)
6vm6_1_H
Sequence is too short. (< 5 resolved nts)
6ywo_1_I
Sequence is too short. (< 5 resolved nts)
2a1r_1_C
Sequence is too short. (< 5 resolved nts)
6m6v_1_F
Sequence is too short. (< 5 resolved nts)
6m6v_1_E
Sequence is too short. (< 5 resolved nts)
2a1r_1_D
Sequence is too short. (< 5 resolved nts)
3gpq_1_E
Sequence is too short. (< 5 resolved nts)
3gpq_1_F
Sequence is too short. (< 5 resolved nts)
6o79_1_C
Sequence is too short. (< 5 resolved nts)
6vm6_1_K
Sequence is too short. (< 5 resolved nts)
6m6v_1_G
Sequence is too short. (< 5 resolved nts)
6hyu_1_D
Sequence is too short. (< 5 resolved nts)
1laj_1_R
Sequence is too short. (< 5 resolved nts)
6ybv_1_K
Could not find nucleotides of chain K in annotation 6ybv.json. Either there is a problem with 6ybv mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
6sce_1_B
Sequence is too short. (< 5 resolved nts)
6xl1_1_C
Sequence is too short. (< 5 resolved nts)
6scf_1_I
Sequence is too short. (< 5 resolved nts)
6scf_1_K
Sequence is too short. (< 5 resolved nts)
6yud_1_K
Sequence is too short. (< 5 resolved nts)
6yud_1_O
Sequence is too short. (< 5 resolved nts)
6scf_1_M
......@@ -2423,7 +2195,7 @@ Sequence is too short. (< 5 resolved nts)
Sequence is too short. (< 5 resolved nts)
1y1y_1_P
DSSR warning 1y1y.json: no nucleotides found. Ignoring 1y1y_1_P.
Sequence is too short. (< 5 resolved nts)
5zuu_1_I
Sequence is too short. (< 5 resolved nts)
......@@ -2431,6 +2203,9 @@ Sequence is too short. (< 5 resolved nts)
5zuu_1_G
Sequence is too short. (< 5 resolved nts)
7am2_1_R1
Sequence is too short. (< 5 resolved nts)
4peh_1_W
Sequence is too short. (< 5 resolved nts)
......@@ -2443,7 +2218,7 @@ Sequence is too short. (< 5 resolved nts)
4peh_1_Y
Sequence is too short. (< 5 resolved nts)
4peh_1_Z
7d8c_1_C
Sequence is too short. (< 5 resolved nts)
6mkn_1_W
......@@ -2458,18 +2233,6 @@ Could not find nucleotides of chain C in annotation 4cxg.json. Either there is a
4cxh_1_C
Could not find nucleotides of chain C in annotation 4cxh.json. Either there is a problem with 4cxh mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
1x1l_1_A
DSSR warning 1x1l.json: no nucleotides found. Ignoring 1x1l_1_A.
1zc8_1_Z
DSSR warning 1zc8.json: no nucleotides found. Ignoring 1zc8_1_Z.
2ob7_1_D
DSSR warning 2ob7.json: no nucleotides found. Ignoring 2ob7_1_D.
2ob7_1_A
DSSR warning 2ob7.json: no nucleotides found. Ignoring 2ob7_1_A.
4eya_1_E
Could not find nucleotides of chain E in annotation 4eya.json. Either there is a problem with 4eya mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
......@@ -2482,30 +2245,6 @@ Could not find nucleotides of chain Q in annotation 4eya.json. Either there is a
4eya_1_R
Could not find nucleotides of chain R in annotation 4eya.json. Either there is a problem with 4eya mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
1qzc_1_B
DSSR warning 1qzc.json: no nucleotides found. Ignoring 1qzc_1_B.
1t1o_1_B
DSSR warning 1t1o.json: no nucleotides found. Ignoring 1t1o_1_B.
1mvr_1_C
DSSR warning 1mvr.json: no nucleotides found. Ignoring 1mvr_1_C.
1t1m_1_B
DSSR warning 1t1m.json: no nucleotides found. Ignoring 1t1m_1_B.
1t1o_1_C
DSSR warning 1t1o.json: no nucleotides found. Ignoring 1t1o_1_C.
1t1m_1_A
DSSR warning 1t1m.json: no nucleotides found. Ignoring 1t1m_1_A.
1t1o_1_A
DSSR warning 1t1o.json: no nucleotides found. Ignoring 1t1o_1_A.
2r1g_1_B
DSSR warning 2r1g.json: no nucleotides found. Ignoring 2r1g_1_B.
4ht9_1_E
Sequence is too short. (< 5 resolved nts)
......@@ -2536,21 +2275,15 @@ Could not find nucleotides of chain U in annotation 5uk4.json. Either there is a
5f6c_1_E
Sequence is too short. (< 5 resolved nts)
7nwh_1_HH
Could not find nucleotides of chain HH in annotation 7nwh.json. Either there is a problem with 7nwh mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
4rcj_1_B
Sequence is too short. (< 5 resolved nts)
1xnr_1_W
Sequence is too short. (< 5 resolved nts)
2agn_1_A
DSSR warning 2agn.json: no nucleotides found. Ignoring 2agn_1_A.
2agn_1_C
DSSR warning 2agn.json: no nucleotides found. Ignoring 2agn_1_C.
2agn_1_B
DSSR warning 2agn.json: no nucleotides found. Ignoring 2agn_1_B.
6e0o_1_C
Sequence is too short. (< 5 resolved nts)
......@@ -2566,15 +2299,6 @@ Sequence is too short. (< 5 resolved nts)
3j06_1_R
Sequence is too short. (< 5 resolved nts)
1r2x_1_C
DSSR warning 1r2x.json: no nucleotides found. Ignoring 1r2x_1_C.
1r2w_1_C
DSSR warning 1r2w.json: no nucleotides found. Ignoring 1r2w_1_C.
1eg0_1_L
DSSR warning 1eg0.json: no nucleotides found. Ignoring 1eg0_1_L.
4eya_1_G
Could not find nucleotides of chain G in annotation 4eya.json. Either there is a problem with 4eya mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
......@@ -2602,11 +2326,8 @@ Sequence is too short. (< 5 resolved nts)
4d61_1_J
Could not find nucleotides of chain J in annotation 4d61.json. Either there is a problem with 4d61 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
1trj_1_B
DSSR warning 1trj.json: no nucleotides found. Ignoring 1trj_1_B.
1trj_1_C
DSSR warning 1trj.json: no nucleotides found. Ignoring 1trj_1_C.
7nwg_1_Q3
Could not find nucleotides of chain Q3 in annotation 7nwg.json. Either there is a problem with 7nwg mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
5tbw_1_SR
Could not find nucleotides of chain SR in annotation 5tbw.json. Either there is a problem with 5tbw mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
......@@ -2731,30 +2452,12 @@ Could not find nucleotides of chain Z in annotation 5flx.json. Either there is a
6eri_1_AX
Could not find nucleotides of chain AX in annotation 6eri.json. Either there is a problem with 6eri mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7k5l_1_R
Sequence is too short. (< 5 resolved nts)
7d80_1_Y
Could not find nucleotides of chain Y in annotation 7d80.json. Either there is a problem with 7d80 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
1zc8_1_A
DSSR warning 1zc8.json: no nucleotides found. Ignoring 1zc8_1_A.
1zc8_1_C
DSSR warning 1zc8.json: no nucleotides found. Ignoring 1zc8_1_C.
1zc8_1_B
DSSR warning 1zc8.json: no nucleotides found. Ignoring 1zc8_1_B.
1zc8_1_G
DSSR warning 1zc8.json: no nucleotides found. Ignoring 1zc8_1_G.
1zc8_1_I
DSSR warning 1zc8.json: no nucleotides found. Ignoring 1zc8_1_I.
1zc8_1_H
DSSR warning 1zc8.json: no nucleotides found. Ignoring 1zc8_1_H.
1zc8_1_J
DSSR warning 1zc8.json: no nucleotides found. Ignoring 1zc8_1_J.
7du2_1_R
Sequence is too short. (< 5 resolved nts)
......@@ -2794,9 +2497,6 @@ Sequence is too short. (< 5 resolved nts)
6sty_1_F
Sequence is too short. (< 5 resolved nts)
2xs5_1_D
Sequence is too short. (< 5 resolved nts)
3ok4_1_N
Could not find nucleotides of chain N in annotation 3ok4.json. Either there is a problem with 3ok4 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
......@@ -2923,12 +2623,6 @@ Sequence is too short. (< 5 resolved nts)
3ol8_1_P
Sequence is too short. (< 5 resolved nts)
1qzc_1_C
DSSR warning 1qzc.json: no nucleotides found. Ignoring 1qzc_1_C.
1qzc_1_A
DSSR warning 1qzc.json: no nucleotides found. Ignoring 1qzc_1_A.
6yrq_1_E
Sequence is too short. (< 5 resolved nts)
......@@ -2947,9 +2641,6 @@ Sequence is too short. (< 5 resolved nts)
6yrb_1_D
Sequence is too short. (< 5 resolved nts)
1mvr_1_D
DSSR warning 1mvr.json: no nucleotides found. Ignoring 1mvr_1_D.
6gz5_1_BV
Could not find nucleotides of chain BV in annotation 6gz5.json. Either there is a problem with 6gz5 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
......@@ -2962,6 +2653,9 @@ Could not find nucleotides of chain BV in annotation 6gz3.json. Either there is
6fti_1_Q
Could not find nucleotides of chain Q in annotation 6fti.json. Either there is a problem with 6fti mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7njc_1_B
Sequence is too short. (< 5 resolved nts)
4v7e_1_AB
Could not find nucleotides of chain AB in annotation 4v7e.json. Either there is a problem with 4v7e mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
......@@ -2995,15 +2689,9 @@ Sequence is too short. (< 5 resolved nts)
1xmo_1_W
Sequence is too short. (< 5 resolved nts)
4adx_1_9
DSSR warning 4adx.json: no nucleotides found. Ignoring 4adx_1_9.
6kr6_1_B
Sequence is too short. (< 5 resolved nts)
1zn1_1_B
DSSR warning 1zn1.json: no nucleotides found. Ignoring 1zn1_1_B.
6z8k_1_X
Sequence is too short. (< 5 resolved nts)
......@@ -3079,9 +2767,6 @@ Sequence is too short. (< 5 resolved nts)
2vrt_1_G
Sequence is too short. (< 5 resolved nts)
1emi_1_B
DSSR warning 1emi.json: no nucleotides found. Ignoring 1emi_1_B.
6r9m_1_B
Sequence is too short. (< 5 resolved nts)
......@@ -3157,9 +2842,6 @@ Sequence is too short. (< 5 resolved nts)
1uvn_1_D
Sequence is too short. (< 5 resolved nts)
3iy9_1_A
DSSR warning 3iy9.json: no nucleotides found. Ignoring 3iy9_1_A.
4wtk_1_T
Sequence is too short. (< 5 resolved nts)
......@@ -3175,63 +2857,9 @@ Sequence is too short. (< 5 resolved nts)
4oav_1_A
Sequence is too short. (< 5 resolved nts)
3ep2_1_E
DSSR warning 3ep2.json: no nucleotides found. Ignoring 3ep2_1_E.
3eq3_1_E
DSSR warning 3eq3.json: no nucleotides found. Ignoring 3eq3_1_E.
3eq4_1_E
DSSR warning 3eq4.json: no nucleotides found. Ignoring 3eq4_1_E.
3ep2_1_A
DSSR warning 3ep2.json: no nucleotides found. Ignoring 3ep2_1_A.
3eq3_1_A
DSSR warning 3eq3.json: no nucleotides found. Ignoring 3eq3_1_A.
3eq4_1_A
DSSR warning 3eq4.json: no nucleotides found. Ignoring 3eq4_1_A.
3ep2_1_C
DSSR warning 3ep2.json: no nucleotides found. Ignoring 3ep2_1_C.
3eq3_1_C
DSSR warning 3eq3.json: no nucleotides found. Ignoring 3eq3_1_C.
3eq4_1_C
DSSR warning 3eq4.json: no nucleotides found. Ignoring 3eq4_1_C.
3ep2_1_B
DSSR warning 3ep2.json: no nucleotides found. Ignoring 3ep2_1_B.
3eq3_1_B
DSSR warning 3eq3.json: no nucleotides found. Ignoring 3eq3_1_B.
3eq4_1_B
DSSR warning 3eq4.json: no nucleotides found. Ignoring 3eq4_1_B.
4i67_1_B
Sequence is too short. (< 5 resolved nts)
3pgw_1_R
DSSR warning 3pgw.json: no nucleotides found. Ignoring 3pgw_1_R.
3pgw_1_N
DSSR warning 3pgw.json: no nucleotides found. Ignoring 3pgw_1_N.
3cw1_1_X
DSSR warning 3cw1.json: no nucleotides found. Ignoring 3cw1_1_X.
3cw1_1_W
DSSR warning 3cw1.json: no nucleotides found. Ignoring 3cw1_1_W.
3cw1_1_V
DSSR warning 3cw1.json: no nucleotides found. Ignoring 3cw1_1_V.
7b0y_1_A
Could not find nucleotides of chain A in annotation 7b0y.json. Either there is a problem with 7b0y mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
6k32_1_T
Could not find nucleotides of chain T in annotation 6k32.json. Either there is a problem with 6k32 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
......@@ -3244,15 +2872,6 @@ Could not find nucleotides of chain A in annotation 5mmj.json. Either there is a
5x8r_1_A
Could not find nucleotides of chain A in annotation 5x8r.json. Either there is a problem with 5x8r mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
2agn_1_E
DSSR warning 2agn.json: no nucleotides found. Ignoring 2agn_1_E.
2agn_1_D
DSSR warning 2agn.json: no nucleotides found. Ignoring 2agn_1_D.
4v5z_1_BD
DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_BD.
6yw5_1_AA
Could not find nucleotides of chain AA in annotation 6yw5.json. Either there is a problem with 6yw5 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
......@@ -3271,8 +2890,8 @@ Sequence is too short. (< 5 resolved nts)
3nvk_1_S
Sequence is too short. (< 5 resolved nts)
2iy3_1_B
DSSR warning 2iy3.json: no nucleotides found. Ignoring 2iy3_1_B.
1cwp_1_D
Sequence is too short. (< 5 resolved nts)
1cwp_1_F
Sequence is too short. (< 5 resolved nts)
......@@ -3391,9 +3010,6 @@ Could not find nucleotides of chain F in annotation 7a09.json. Either there is a
5t2c_1_AN
Could not find nucleotides of chain AN in annotation 5t2c.json. Either there is a problem with 5t2c mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
4v5z_1_BF
DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_BF.
3j6b_1_E
Could not find nucleotides of chain E in annotation 3j6b.json. Either there is a problem with 3j6b mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
......@@ -3463,6 +3079,18 @@ Sequence is too short. (< 5 resolved nts)
4v4f_1_B2
Sequence is too short. (< 5 resolved nts)
7m4y_1_V
Could not find nucleotides of chain V in annotation 7m4y.json. Either there is a problem with 7m4y mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7m4x_1_V
Could not find nucleotides of chain V in annotation 7m4x.json. Either there is a problem with 7m4x mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
6v3a_1_V
Could not find nucleotides of chain V in annotation 6v3a.json. Either there is a problem with 6v3a mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
6v39_1_V
Could not find nucleotides of chain V in annotation 6v39.json. Either there is a problem with 6v39 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
5it9_1_I
Could not find nucleotides of chain I in annotation 5it9.json. Either there is a problem with 5it9 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
......@@ -3481,18 +3109,9 @@ Sequence is too short. (< 5 resolved nts)
5zsn_1_E
Sequence is too short. (< 5 resolved nts)
1cwp_1_D
Sequence is too short. (< 5 resolved nts)
3jcr_1_N
DSSR warning 3jcr.json: no nucleotides found. Ignoring 3jcr_1_N.
6gfw_1_R
Sequence is too short. (< 5 resolved nts)
2vaz_1_A
DSSR warning 2vaz.json: no nucleotides found. Ignoring 2vaz_1_A.
6zm6_1_X
Could not find nucleotides of chain X in annotation 6zm6.json. Either there is a problem with 6zm6 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
......@@ -3505,9 +3124,6 @@ Could not find nucleotides of chain W in annotation 6zm6.json. Either there is a
6zm5_1_W
Could not find nucleotides of chain W in annotation 6zm5.json. Either there is a problem with 6zm5 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
4v5z_1_BP
DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_BP.
6n6e_1_D
Sequence is too short. (< 5 resolved nts)
......@@ -3535,9 +3151,6 @@ Sequence is too short. (< 5 resolved nts)
5uh9_1_I
Sequence is too short. (< 5 resolved nts)
2ftc_1_R
DSSR warning 2ftc.json: no nucleotides found. Ignoring 2ftc_1_R.
7a5j_1_X
Could not find nucleotides of chain X in annotation 7a5j.json. Either there is a problem with 7a5j mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
......@@ -3547,9 +3160,6 @@ Sequence is too short. (< 5 resolved nts)
4udv_1_R
Sequence is too short. (< 5 resolved nts)
2r1g_1_E
DSSR warning 2r1g.json: no nucleotides found. Ignoring 2r1g_1_E.
5zsc_1_D
Sequence is too short. (< 5 resolved nts)
......@@ -3631,9 +3241,6 @@ Sequence is too short. (< 5 resolved nts)
3m85_1_Y
Sequence is too short. (< 5 resolved nts)
1e8s_1_C
DSSR warning 1e8s.json: no nucleotides found. Ignoring 1e8s_1_C.
5wnp_1_B
Could not find nucleotides of chain B in annotation 5wnp.json. Either there is a problem with 5wnp mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
......@@ -3700,12 +3307,21 @@ Sequence is too short. (< 5 resolved nts)
3u2e_1_C
Sequence is too short. (< 5 resolved nts)
7eh1_1_I
Sequence is too short. (< 5 resolved nts)
5uef_1_C
Sequence is too short. (< 5 resolved nts)
5uef_1_D
Sequence is too short. (< 5 resolved nts)
7eh2_1_R
Sequence is too short. (< 5 resolved nts)
7eh2_1_I
Sequence is too short. (< 5 resolved nts)
4x4u_1_H
Sequence is too short. (< 5 resolved nts)
......@@ -3751,12 +3367,6 @@ Sequence is too short. (< 5 resolved nts)
4k4t_1_D
Sequence is too short. (< 5 resolved nts)
1zn1_1_C
DSSR warning 1zn1.json: no nucleotides found. Ignoring 1zn1_1_C.
1zn0_1_C
DSSR warning 1zn0.json: no nucleotides found. Ignoring 1zn0_1_C.
1xpu_1_G
Sequence is too short. (< 5 resolved nts)
......@@ -3829,6 +3439,9 @@ Sequence is too short. (< 5 resolved nts)
1n1h_1_B
Sequence is too short. (< 5 resolved nts)
7n2v_1_PT
Could not find nucleotides of chain PT in annotation 7n2v.json. Either there is a problem with 7n2v mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
4ohz_1_B
Sequence is too short. (< 5 resolved nts)
......@@ -3865,15 +3478,9 @@ Sequence is too short. (< 5 resolved nts)
4gkj_1_W
Sequence is too short. (< 5 resolved nts)
4v5z_1_BC
DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_BC.
5y88_1_X
Could not find nucleotides of chain X in annotation 5y88.json. Either there is a problem with 5y88 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
4v5z_1_BB
DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_BB.
3j0o_1_H
Could not find nucleotides of chain H in annotation 3j0o.json. Either there is a problem with 3j0o mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
......@@ -3886,9 +3493,6 @@ Could not find nucleotides of chain H in annotation 3j0p.json. Either there is a
3j0q_1_H
Could not find nucleotides of chain H in annotation 3j0q.json. Either there is a problem with 3j0q mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
4v5z_1_BH
DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_BH.
3j0o_1_F
Could not find nucleotides of chain F in annotation 3j0o.json. Either there is a problem with 3j0o mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
......@@ -3931,9 +3535,6 @@ Could not find nucleotides of chain A in annotation 3j0q.json. Either there is a
3j0p_1_A
Could not find nucleotides of chain A in annotation 3j0p.json. Either there is a problem with 3j0p mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
4v5z_1_BJ
DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_BJ.
6ys3_1_V
Could not find nucleotides of chain V in annotation 6ys3.json. Either there is a problem with 6ys3 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
......@@ -4039,15 +3640,9 @@ Could not find nucleotides of chain BB in annotation 5mre.json. Either there is
5mrf_1_BB
Could not find nucleotides of chain BB in annotation 5mrf.json. Either there is a problem with 5mrf mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
4v5z_1_BN
DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_BN.
3j46_1_P
Could not find nucleotides of chain P in annotation 3j46.json. Either there is a problem with 3j46 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
3jcr_1_M
DSSR warning 3jcr.json: no nucleotides found. Ignoring 3jcr_1_M.
4e6b_1_A
Sequence is too short. (< 5 resolved nts)
......@@ -4057,12 +3652,6 @@ Sequence is too short. (< 5 resolved nts)
6a6l_1_D
Sequence is too short. (< 5 resolved nts)
4v5z_1_BS
DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_BS.
4v8t_1_1
Could not find nucleotides of chain 1 in annotation 4v8t.json. Either there is a problem with 4v8t mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
1uvi_1_D
Sequence is too short. (< 5 resolved nts)
......@@ -4132,17 +3721,8 @@ Could not find nucleotides of chain 2M in annotation 6ip6.json. Either there is
6qcs_1_M
Sequence is too short. (< 5 resolved nts)
486d_1_G
Could not find nucleotides of chain G in annotation 486d.json. Either there is a problem with 486d mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
2r1g_1_C
DSSR warning 2r1g.json: no nucleotides found. Ignoring 2r1g_1_C.
486d_1_F
Could not find nucleotides of chain F in annotation 486d.json. Either there is a problem with 486d mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
4v5z_1_B0
DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_B0.
7b5k_1_Z
Could not find nucleotides of chain Z in annotation 7b5k.json. Either there is a problem with 7b5k mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
4nia_1_O
Could not find nucleotides of chain O in annotation 4nia.json. Either there is a problem with 4nia mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
......@@ -4177,6 +3757,9 @@ Could not find nucleotides of chain L in annotation 4oq9.json. Either there is a
6r9q_1_B
Sequence is too short. (< 5 resolved nts)
7m4u_1_A
Could not find nucleotides of chain A in annotation 7m4u.json. Either there is a problem with 7m4u mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
6v3a_1_SN1
Could not find nucleotides of chain SN1 in annotation 6v3a.json. Either there is a problem with 6v3a mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
......@@ -4189,15 +3772,6 @@ Could not find nucleotides of chain SN1 in annotation 6v39.json. Either there is
6v3e_1_SN1
Could not find nucleotides of chain SN1 in annotation 6v3e.json. Either there is a problem with 6v3e mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
1pn7_1_C
DSSR warning 1pn7.json: no nucleotides found. Ignoring 1pn7_1_C.
1mj1_1_Q
Could not find nucleotides of chain Q in annotation 1mj1.json. Either there is a problem with 1mj1 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
1mj1_1_R
Could not find nucleotides of chain R in annotation 1mj1.json. Either there is a problem with 1mj1 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
4dr6_1_V
Sequence is too short. (< 5 resolved nts)
......@@ -4315,26 +3889,47 @@ Sequence is too short. (< 5 resolved nts)
6oy6_1_I
Sequence is too short. (< 5 resolved nts)
4bbl_1_Y
DSSR warning 4bbl.json: no nucleotides found. Ignoring 4bbl_1_Y.
4bbl_1_Z
DSSR warning 4bbl.json: no nucleotides found. Ignoring 4bbl_1_Z.
4qvd_1_H
Sequence is too short. (< 5 resolved nts)
5gxi_1_B
Sequence is too short. (< 5 resolved nts)
3iy8_1_A
DSSR warning 3iy8.json: no nucleotides found. Ignoring 3iy8_1_A.
7n06_1_G
Sequence is too short. (< 5 resolved nts)
6tnu_1_M
Could not find nucleotides of chain M in annotation 6tnu.json. Either there is a problem with 6tnu mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7n06_1_H
Sequence is too short. (< 5 resolved nts)
5mc6_1_M
Could not find nucleotides of chain M in annotation 5mc6.json. Either there is a problem with 5mc6 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7n06_1_I
Sequence is too short. (< 5 resolved nts)
7n06_1_J
Sequence is too short. (< 5 resolved nts)
7n06_1_K
Sequence is too short. (< 5 resolved nts)
7n06_1_L
Sequence is too short. (< 5 resolved nts)
7n33_1_G
Sequence is too short. (< 5 resolved nts)
7n33_1_H
Sequence is too short. (< 5 resolved nts)
7n33_1_I
Sequence is too short. (< 5 resolved nts)
7n33_1_J
Sequence is too short. (< 5 resolved nts)
7n33_1_K
Sequence is too short. (< 5 resolved nts)
7n33_1_L
Sequence is too short. (< 5 resolved nts)
5mc6_1_N
Could not find nucleotides of chain N in annotation 5mc6.json. Either there is a problem with 5mc6 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
......@@ -4363,12 +3958,6 @@ Could not find nucleotides of chain U in annotation 6htq.json. Either there is a
6uu6_1_333
Sequence is too short. (< 5 resolved nts)
6v3a_1_V
Could not find nucleotides of chain V in annotation 6v3a.json. Either there is a problem with 6v3a mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
6v39_1_V
Could not find nucleotides of chain V in annotation 6v39.json. Either there is a problem with 6v39 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
5a0v_1_F
Sequence is too short. (< 5 resolved nts)
......@@ -4387,63 +3976,9 @@ Sequence is too short. (< 5 resolved nts)
5wnu_1_B
Could not find nucleotides of chain B in annotation 5wnu.json. Either there is a problem with 5wnu mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
1zc8_1_F
DSSR warning 1zc8.json: no nucleotides found. Ignoring 1zc8_1_F.
1vtm_1_R
Sequence is too short. (< 5 resolved nts)
4v5z_1_BA
DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_BA.
4v5z_1_BE
DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_BE.
4v5z_1_BG
DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_BG.
4v5z_1_BI
DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_BI.
4v5z_1_BK
DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_BK.
4v5z_1_BM
DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_BM.
4v5z_1_BL
DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_BL.
4v5z_1_BV
DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_BV.
4v5z_1_BO
DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_BO.
4v5z_1_BQ
DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_BQ.
4v5z_1_BR
DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_BR.
4v5z_1_BT
DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_BT.
4v5z_1_BU
DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_BU.
4v5z_1_BW
DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_BW.
4v5z_1_BY
DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_BY.
4v5z_1_BX
DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_BX.
4v5z_1_BZ
DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_BZ.
5elt_1_F
Sequence is too short. (< 5 resolved nts)
......@@ -4480,9 +4015,6 @@ Could not find nucleotides of chain B in annotation 4cxg.json. Either there is a
4cxh_1_B
Could not find nucleotides of chain B in annotation 4cxh.json. Either there is a problem with 4cxh mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
4v5z_1_B1
DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_B1.
5z4d_1_B
Sequence is too short. (< 5 resolved nts)
......@@ -4495,6 +4027,9 @@ Could not find nucleotides of chain BV in annotation 6xa1.json. Either there is
6ha8_1_X
Could not find nucleotides of chain X in annotation 6ha8.json. Either there is a problem with 6ha8 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
2xs5_1_D
Sequence is too short. (< 5 resolved nts)
1m8w_1_E
Could not find nucleotides of chain E in annotation 1m8w.json. Either there is a problem with 1m8w mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
......@@ -4579,6 +4114,15 @@ Sequence is too short. (< 5 resolved nts)
1qln_1_R
Sequence is too short. (< 5 resolved nts)
3cw1_1_X
Could not find nucleotides of chain X in annotation 3cw1.json. Either there is a problem with 3cw1 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
3cw1_1_W
Could not find nucleotides of chain W in annotation 3cw1.json. Either there is a problem with 3cw1 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7b0y_1_A
Could not find nucleotides of chain A in annotation 7b0y.json. Either there is a problem with 7b0y mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
6ogy_1_M
Sequence is too short. (< 5 resolved nts)
......@@ -4591,9 +4135,6 @@ Sequence is too short. (< 5 resolved nts)
6ywy_1_BB
Could not find nucleotides of chain BB in annotation 6ywy.json. Either there is a problem with 6ywy mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
1x18_1_A
DSSR warning 1x18.json: no nucleotides found. Ignoring 1x18_1_A.
5ytx_1_B
Sequence is too short. (< 5 resolved nts)
......@@ -4681,21 +4222,6 @@ Could not find nucleotides of chain W in annotation 5lzb.json. Either there is a
3wzi_1_C
Sequence is too short. (< 5 resolved nts)
1mvr_1_E
DSSR warning 1mvr.json: no nucleotides found. Ignoring 1mvr_1_E.
1mvr_1_B
DSSR warning 1mvr.json: no nucleotides found. Ignoring 1mvr_1_B.
1mvr_1_A
DSSR warning 1mvr.json: no nucleotides found. Ignoring 1mvr_1_A.
4adx_1_0
DSSR warning 4adx.json: no nucleotides found. Ignoring 4adx_1_0.
4adx_1_8
DSSR warning 4adx.json: no nucleotides found. Ignoring 4adx_1_8.
1n33_1_Z
Sequence is too short. (< 5 resolved nts)
......@@ -4720,24 +4246,9 @@ Could not find nucleotides of chain AA in annotation 5mrf.json. Either there is
7jhy_1_Z
Could not find nucleotides of chain Z in annotation 7jhy.json. Either there is a problem with 7jhy mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
2r1g_1_A
DSSR warning 2r1g.json: no nucleotides found. Ignoring 2r1g_1_A.
2r1g_1_D
DSSR warning 2r1g.json: no nucleotides found. Ignoring 2r1g_1_D.
2r1g_1_F
DSSR warning 2r1g.json: no nucleotides found. Ignoring 2r1g_1_F.
3eq4_1_Y
DSSR warning 3eq4.json: no nucleotides found. Ignoring 3eq4_1_Y.
4wkr_1_C
Sequence is too short. (< 5 resolved nts)
2r1g_1_X
DSSR warning 2r1g.json: no nucleotides found. Ignoring 2r1g_1_X.
4v99_1_EC
Could not find nucleotides of chain EC in annotation 4v99.json. Either there is a problem with 4v99 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
......@@ -4945,102 +4456,6 @@ Sequence is too short. (< 5 resolved nts)
4qvc_1_G
Sequence is too short. (< 5 resolved nts)
6q1h_1_D
Sequence is too short. (< 5 resolved nts)
6q1h_1_H
Sequence is too short. (< 5 resolved nts)
6p7p_1_F
Sequence is too short. (< 5 resolved nts)
6p7p_1_E
Sequence is too short. (< 5 resolved nts)
6p7p_1_D
Sequence is too short. (< 5 resolved nts)
6vm6_1_J
Sequence is too short. (< 5 resolved nts)
6vm6_1_G
Sequence is too short. (< 5 resolved nts)
6wan_1_K
Sequence is too short. (< 5 resolved nts)
6wan_1_H
Sequence is too short. (< 5 resolved nts)
6wan_1_G
Sequence is too short. (< 5 resolved nts)
6wan_1_L
Sequence is too short. (< 5 resolved nts)
6wan_1_I
Sequence is too short. (< 5 resolved nts)
6ywo_1_F
Sequence is too short. (< 5 resolved nts)
6wan_1_J
Sequence is too short. (< 5 resolved nts)
4oau_1_A
Sequence is too short. (< 5 resolved nts)
6ywo_1_E
Sequence is too short. (< 5 resolved nts)
6ywo_1_K
Sequence is too short. (< 5 resolved nts)
6vm6_1_I
Sequence is too short. (< 5 resolved nts)
6vm6_1_H
Sequence is too short. (< 5 resolved nts)
6ywo_1_I
Sequence is too short. (< 5 resolved nts)
2a1r_1_C
Sequence is too short. (< 5 resolved nts)
6m6v_1_F
Sequence is too short. (< 5 resolved nts)
6m6v_1_E
Sequence is too short. (< 5 resolved nts)
2a1r_1_D
Sequence is too short. (< 5 resolved nts)
3gpq_1_E
Sequence is too short. (< 5 resolved nts)
3gpq_1_F
Sequence is too short. (< 5 resolved nts)
6o79_1_C
Sequence is too short. (< 5 resolved nts)
6vm6_1_K
Sequence is too short. (< 5 resolved nts)
6m6v_1_G
Sequence is too short. (< 5 resolved nts)
6hyu_1_D
Sequence is too short. (< 5 resolved nts)
1laj_1_R
Sequence is too short. (< 5 resolved nts)
6ybv_1_K
Could not find nucleotides of chain K in annotation 6ybv.json. Either there is a problem with 6ybv mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
6mpf_1_W
Sequence is too short. (< 5 resolved nts)
......@@ -5080,15 +4495,6 @@ Sequence is too short. (< 5 resolved nts)
5hkc_1_C
Sequence is too short. (< 5 resolved nts)
4kzy_1_I
Could not find nucleotides of chain I in annotation 4kzy.json. Either there is a problem with 4kzy mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
4kzz_1_I
Could not find nucleotides of chain I in annotation 4kzz.json. Either there is a problem with 4kzz mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
4kzx_1_I
Could not find nucleotides of chain I in annotation 4kzx.json. Either there is a problem with 4kzx mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
1rmv_1_B
Sequence is too short. (< 5 resolved nts)
......@@ -5101,30 +4507,6 @@ Sequence is too short. (< 5 resolved nts)
4qu7_1_U
Sequence is too short. (< 5 resolved nts)
4v5z_1_AH
DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_AH.
4v5z_1_AA
DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_AA.
4v5z_1_AB
DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_AB.
4v5z_1_AC
DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_AC.
4v5z_1_AD
DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_AD.
4v5z_1_AE
DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_AE.
4v5z_1_AF
DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_AF.
4v5z_1_AG
DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_AG.
6pmi_1_3
Sequence is too short. (< 5 resolved nts)
......@@ -5134,69 +4516,81 @@ Sequence is too short. (< 5 resolved nts)
5hjz_1_C
Sequence is too short. (< 5 resolved nts)
7nrc_1_SM
Could not find nucleotides of chain SM in annotation 7nrc.json. Either there is a problem with 7nrc mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
6ydp_1_AA_1176-2737
Could not find nucleotides of chain AA in annotation 6ydp.json. Either there is a problem with 6ydp mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7nrc_1_SN
Could not find nucleotides of chain SN in annotation 7nrc.json. Either there is a problem with 7nrc mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
6ydw_1_AA_1176-2737
Could not find nucleotides of chain AA in annotation 6ydw.json. Either there is a problem with 6ydw mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7am2_1_R1
1vy7_1_AY_1-73
Sequence is too short. (< 5 resolved nts)
7k5l_1_R
1vy7_1_CY_1-73
Sequence is too short. (< 5 resolved nts)
7b5k_1_X
Could not find nucleotides of chain X in annotation 7b5k.json. Either there is a problem with 7b5k mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7d8c_1_C
4w2h_1_CY_1-73
Sequence is too short. (< 5 resolved nts)
7m4y_1_V
Could not find nucleotides of chain V in annotation 7m4y.json. Either there is a problem with 7m4y mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7d1a_1_A_805-902
Could not find nucleotides of chain A in annotation 7d1a.json. Either there is a problem with 7d1a mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7m4x_1_V
Could not find nucleotides of chain V in annotation 7m4x.json. Either there is a problem with 7m4x mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7d0g_1_A_805-913
Could not find nucleotides of chain A in annotation 7d0g.json. Either there is a problem with 7d0g mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7b5k_1_Z
Could not find nucleotides of chain Z in annotation 7b5k.json. Either there is a problem with 7b5k mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7d0f_1_A_817-913
Could not find nucleotides of chain A in annotation 7d0f.json. Either there is a problem with 7d0f mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7m4u_1_A
Could not find nucleotides of chain A in annotation 7m4u.json. Either there is a problem with 7m4u mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7o7z_1_AH_144-220
Could not find nucleotides of chain AH in annotation 7o7z.json. Either there is a problem with 7o7z mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7n06_1_G
Sequence is too short. (< 5 resolved nts)
4c9d_1_D_29-1
Mapping is reversed, this case is not supported (yet).
7n06_1_H
Sequence is too short. (< 5 resolved nts)
4c9d_1_C_29-1
Mapping is reversed, this case is not supported (yet).
7n06_1_I
Sequence is too short. (< 5 resolved nts)
7aih_1_1_2400-2963
Could not find nucleotides of chain 1 in annotation 7aih.json. Either there is a problem with 7aih mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7n06_1_J
Sequence is too short. (< 5 resolved nts)
7aih_1_1_2984-3610
Could not find nucleotides of chain 1 in annotation 7aih.json. Either there is a problem with 7aih mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7n06_1_K
Sequence is too short. (< 5 resolved nts)
7ane_1_2_1904-2468
Could not find nucleotides of chain 2 in annotation 7ane.json. Either there is a problem with 7ane mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7n06_1_L
Sequence is too short. (< 5 resolved nts)
7ane_1_2_2489-3115
Could not find nucleotides of chain 2 in annotation 7ane.json. Either there is a problem with 7ane mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7n33_1_G
5g2x_1_A_595-692
Sequence is too short. (< 5 resolved nts)
7n33_1_H
Sequence is too short. (< 5 resolved nts)
7aor_1_2_2020-2579
Could not find nucleotides of chain 2 in annotation 7aor.json. Either there is a problem with 7aor mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7n33_1_I
Sequence is too short. (< 5 resolved nts)
7aor_1_2_2589-3210
Could not find nucleotides of chain 2 in annotation 7aor.json. Either there is a problem with 7aor mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7n33_1_J
Sequence is too short. (< 5 resolved nts)
7a5p_1_2_259-449
Could not find nucleotides of chain 2 in annotation 7a5p.json. Either there is a problem with 7a5p mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7n33_1_K
Sequence is too short. (< 5 resolved nts)
7aor_1_A_2020-2579
Could not find nucleotides of chain A in annotation 7aor.json. Either there is a problem with 7aor mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7n33_1_L
Sequence is too short. (< 5 resolved nts)
7aor_1_A_2589-3210
Could not find nucleotides of chain A in annotation 7aor.json. Either there is a problem with 7aor mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7am2_1_1_1904-2470
Could not find nucleotides of chain 1 in annotation 7am2.json. Either there is a problem with 7am2 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7am2_1_1_2491-3117
Could not find nucleotides of chain 1 in annotation 7am2.json. Either there is a problem with 7am2 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7ane_1_1_1904-2468
Could not find nucleotides of chain 1 in annotation 7ane.json. Either there is a problem with 7ane mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7ane_1_1_2489-3115
Could not find nucleotides of chain 1 in annotation 7ane.json. Either there is a problem with 7ane mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
6uz7_1_8_2140-2825
Could not find nucleotides of chain 8 in annotation 6uz7.json. Either there is a problem with 6uz7 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
......
......@@ -5,7 +5,7 @@ rm -rf latest_run.log errors.txt
# Run RNANet
bash -c 'time python3.8 ./RNAnet.py --3d-folder /home/lbecquey/Data/RNA/3D/ --seq-folder /home/lbecquey/Data/RNA/sequences/ -r 20.0 --no-homology --redundant --extract' > latest_run.log 2>&1
bash -c 'time python3.8 ./RNAnet.py --3d-folder /home/lbecquey/Data/RNA/3D/ --seq-folder /home/lbecquey/Data/RNA/sequences/ -r 20.0 --redundant --sina --extract -s --stats-opts="--wadley --distance-matrices" --archive' > latest_run.log 2>&1
bash -c 'time python3.8 ./RNAnet.py --3d-folder /home/lbecquey/Data/RNA/3D/ --seq-folder /home/lbecquey/Data/RNA/sequences/ -r 20.0 --redundant --extract -s --stats-opts="-r 20.0 --wadley --hire-rna --distance-matrices" --archive' >> latest_run.log 2>&1
echo 'Compressing RNANet.db.gz...' >> latest_run.log
touch results/RNANet.db # update last modification date
gzip -k /home/lbecquey/Projects/RNANet/results/RNANet.db # compress it
......
# This is a script supposed to be run periodically as a cron job
# This one uses argument --from-scratch, so all is recomputed ! /!\
# run it one or twice a year, otherwise, the faster update runs should be enough.
cd /home/lbecquey/Projects/RNANet
rm -rf latest_run.log errors.txt known_issues.txt known_issues_reasons.txt
# Run RNANet
bash -c 'time python3.8 ./RNAnet.py --3d-folder /home/lbecquey/Data/RNA/3D/ --seq-folder /home/lbecquey/Data/RNA/sequences/ --from-scratch --ignore-issues -r 20.0 --no-homology --redundant --extract' > latest_run.log 2>&1
bash -c 'time python3.8 ./RNAnet.py --3d-folder /home/lbecquey/Data/RNA/3D/ --seq-folder /home/lbecquey/Data/RNA/sequences/ --from-scratch --ignore-issues -r 20.0 --redundant --extract -s --stats-opts="-r 20.0 --wadley --hire-rna --distance-matrices" --archive' >> latest_run.log 2>&1
echo 'Compressing RNANet.db.gz...' >> latest_run.log
touch results/RNANet.db # update last modification date
gzip -k /home/lbecquey/Projects/RNANet/results/RNANet.db # compress it
rm -f results/RNANet.db-wal results/RNANet.db-shm # SQLite temporary files
# Save the latest results
export DATE=`date +%Y%m%d`
echo "Creating new release in ./archive/ folder ($DATE)..." >> latest_run.log
cp /home/lbecquey/Projects/RNANet/results/summary.csv /home/lbecquey/Projects/RNANet/archive/summary_latest.csv
cp /home/lbecquey/Projects/RNANet/results/summary.csv "/home/lbecquey/Projects/RNANet/archive/summary_$DATE.csv"
cp /home/lbecquey/Projects/RNANet/results/families.csv /home/lbecquey/Projects/RNANet/archive/families_latest.csv
cp /home/lbecquey/Projects/RNANet/results/families.csv "/home/lbecquey/Projects/RNANet/archive/families_$DATE.csv"
cp /home/lbecquey/Projects/RNANet/results/frequencies.csv /home/lbecquey/Projects/RNANet/archive/frequencies_latest.csv
cp /home/lbecquey/Projects/RNANet/results/pair_types.csv /home/lbecquey/Projects/RNANet/archive/pair_types_latest.csv
mv /home/lbecquey/Projects/RNANet/results/RNANet.db.gz /home/lbecquey/Projects/RNANet/archive/
# Init Seafile synchronization between RNANet library and ./archive/ folder (just the first time !)
# seaf-cli sync -l 8e082c6e-b9ed-4b2f-9279-de2177134c57 -s https://entrepot.ibisc.univ-evry.fr -u l****.b*****y@univ-evry.fr -p ****************** -d archive/
# Sync in Seafile
seaf-cli start >> latest_run.log 2>&1
echo 'Waiting 10m for SeaFile synchronization...' >> latest_run.log
sleep 15m
echo `seaf-cli status` >> latest_run.log
seaf-cli stop >> latest_run.log 2>&1
echo 'We are '`date`', update completed.' >> latest_run.log
......@@ -21,6 +21,6 @@ docker build -t rnanet:latest ..
rm x3dna-dssr
# to run, use something like:
# docker run -v /home/persalteas/Data/RNA/3D/:/3D -v /home/persalteas/Data/RNA/sequences/:/sequences -v /home/persalteas/labo/:/runDir persalteas/rnanet [ additional options here ]
# docker run -v /home/lbecquey/Data/RNA/3D/:/3D -v /home/lbecquey/Data/RNA/sequences/:/sequences -v /home/lbecquey/labo/:/runDir rnanet [ additional options here ]
# Without additional options, this runs a standard pass with known issues support, log output, and no statistics. The default resolution threshold is 4.0 Angstroms.
......
......@@ -36,6 +36,6 @@ for fam in families:
# Now re run RNANet normally.
command = ["python3.8", "./RNAnet.py", "--3d-folder", path_to_3D_data, "--seq-folder", path_to_seq_data, "-r", "20.0",
"--redundant", "--sina", "--extract", "-s", "--stats-opts=\"--wadley --distance-matrices\""]
"--redundant", "--extract", "-s", "--stats-opts=\"-r 20.0 --wadley --hire-rna --distance-matrices\""]
print(' '.join(command))
subprocess.run(command)
\ No newline at end of file
......
......@@ -3,8 +3,9 @@ import subprocess, os, sys
# Put a list of problematic chains here, they will be properly deleted and recomputed
problems = [
"1k73_1_A",
"1k73_1_B"
"7nhm_1_A_1-2923"
"4wfa_1_X_1-2923"
"4wce_1_X_1-2923"
]
# provide the path to your data folders, the RNANet.db file, and the RNANet.py file as arguments to this script
......@@ -22,6 +23,7 @@ for p in problems:
# Remove the datapoints files and 3D files
subprocess.run(["rm", '-f', path_to_3D_data + f"/rna_mapped_to_Rfam/{p}.cif"])
subprocess.run(["rm", '-f', path_to_3D_data + f"/rna_only/{p}.cif"])
files = [ f for f in os.listdir(path_to_3D_data + "/datapoints") if p in f ]
for f in files:
subprocess.run(["rm", '-f', path_to_3D_data + f"/datapoints/{f}"])
......@@ -38,14 +40,14 @@ for p in problems:
print(' '.join(command))
subprocess.run(command)
command = ["python3.8", path_to_RNANet, "--3d-folder", path_to_3D_data, "--seq-folder", path_to_seq_data, "-r", "20.0", "--extract", "--only", p]
command = ["python3.8", path_to_RNANet, "--3d-folder", path_to_3D_data, "--seq-folder", path_to_seq_data, "--redundant", "-r", "20.0", "--extract", "--only", p]
else:
# Delete the chain from the database, and the associated nucleotides and re_mappings, using foreign keys
command = ["sqlite3", path_to_db, f"PRAGMA foreign_keys=ON; delete from chain where structure_id=\"{structure}\" and chain_name=\"{chain}\" and rfam_acc is null;"]
print(' '.join(command))
subprocess.run(command)
command = ["python3.8", path_to_RNANet, "--3d-folder", path_to_3D_data, "--seq-folder", path_to_seq_data, "-r", "20.0", "--no-homology", "--extract", "--only", p]
command = ["python3.8", path_to_RNANet, "--3d-folder", path_to_3D_data, "--seq-folder", path_to_seq_data, "--redundant", "-r", "20.0", "--no-homology", "--extract", "--only", p]
# Re-run RNANet
os.chdir(os.path.dirname(os.path.realpath(path_to_db)) + '/../')
......
This diff could not be displayed because it is too large.