@@ -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.
@@ -7,12 +7,6 @@ Could not find nucleotides of chain AA in annotation 6ydw.json. Either there is
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.
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.
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.
1qzb_1_B_1-73
DSSR warning 1qzb.json: no nucleotides found. Ignoring 1qzb_1_B_1-73.
DSSR warning 1ls2.json: no nucleotides found. Ignoring 1ls2_1_B_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.
1gsg_1_T_1-72
DSSR warning 1gsg.json: no nucleotides found. Ignoring 1gsg_1_T_1-72.
DSSR warning 4v47.json: no nucleotides found. Ignoring 4v47_1_A9_3-118.
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.
2ob7_1_A_10-319
DSSR warning 2ob7.json: no nucleotides found. Ignoring 2ob7_1_A_10-319.
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.
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.
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.
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.
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...
@@ -157,6 +154,9 @@ Could not find nucleotides of chain A in annotation 1jgo.json. Either there is a
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.
1zc8_1_A_1-59
DSSR warning 1zc8.json: no nucleotides found. Ignoring 1zc8_1_A_1-59.
1mvr_1_D_1-59
DSSR warning 1mvr.json: no nucleotides found. Ignoring 1mvr_1_D_1-59.
DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_B1_2-123.
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.
1mvr_1_B_1-96
DSSR warning 1mvr.json: no nucleotides found. Ignoring 1mvr_1_B_1-96.
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...
@@ -889,9 +889,24 @@ 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.
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...
@@ -1003,6 +1018,54 @@ Could not find nucleotides of chain X in annotation 4v4i.json. Either there is a
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.
4jrc_1_B
Nucleotides not inserted !
4jrc_1_A
Nucleotides not inserted !
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.
6d30_1_C
Sequence is too short. (< 5 resolved nts)
...
...
@@ -1315,62 +1378,53 @@ 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.
4b3r_1_W
Sequence is too short. (< 5 resolved nts)
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.
4b3t_1_W
Sequence is too short. (< 5 resolved nts)
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.
4b3s_1_W
Sequence is too short. (< 5 resolved nts)
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.
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.
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.
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.
3dg2_1_A
DSSR warning 3dg2.json: no nucleotides found. Ignoring 3dg2_1_A.
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.
3dg0_1_A
DSSR warning 3dg0.json: no nucleotides found. Ignoring 3dg0_1_A.
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.
4v48_1_BA
DSSR warning 4v48.json: no nucleotides found. Ignoring 4v48_1_BA.
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.
4v47_1_BA
DSSR warning 4v47.json: no nucleotides found. Ignoring 4v47_1_BA.
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.
3dg4_1_A
DSSR warning 3dg4.json: no nucleotides found. Ignoring 3dg4_1_A.
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.
3dg5_1_A
DSSR warning 3dg5.json: no nucleotides found. Ignoring 3dg5_1_A.
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.
4b3r_1_W
Sequence is too short. (< 5 resolved nts)
6yl5_1_I
Nucleotides not inserted !
4b3t_1_W
Sequence is too short. (< 5 resolved nts)
6yl5_1_E
Nucleotides not inserted !
4b3s_1_W
Sequence is too short. (< 5 resolved nts)
6yl5_1_A
Nucleotides not inserted !
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.
6yl5_1_K
Nucleotides not inserted !
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.
6yl5_1_G
Nucleotides not inserted !
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.
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@@ -1582,6 +1636,9 @@ Could not find nucleotides of chain V in annotation 6olf.json. Either there is a
3erc_1_G
Sequence is too short. (< 5 resolved nts)
4qjd_1_D
Nucleotides not inserted !
6of1_1_1W
Could not find nucleotides of chain 1W in annotation 6of1.json. Either there is a problem with 6of1 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
@@ -1738,18 +1801,15 @@ Could not find nucleotides of chain NB in annotation 6i7o.json. Either there is
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.
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.
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.
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...
@@ -1768,6 +1828,15 @@ 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.
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...
@@ -1780,6 +1849,9 @@ 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.
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.
3jcr_1_H
DSSR warning 3jcr.json: no nucleotides found. Ignoring 3jcr_1_H.
...
...
@@ -2119,9 +2200,6 @@ 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)
...
...
@@ -2236,14 +2314,11 @@ 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)
...
...
@@ -2278,6 +2353,9 @@ Sequence is too short. (< 5 resolved nts)
4xbf_1_D
Sequence is too short. (< 5 resolved nts)
5w1h_1_B
Nucleotides not inserted !
6n6d_1_D
Sequence is too short. (< 5 resolved nts)
...
...
@@ -2296,52 +2374,148 @@ 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)
6scf_1_M
6vm6_1_G
Sequence is too short. (< 5 resolved nts)
6yud_1_P
6wan_1_K
Sequence is too short. (< 5 resolved nts)
6scf_1_L
6wan_1_H
Sequence is too short. (< 5 resolved nts)
6yud_1_M
6wan_1_G
Sequence is too short. (< 5 resolved nts)
6yud_1_Q
6wan_1_L
Sequence is too short. (< 5 resolved nts)
6w11_1_C
6wan_1_I
Sequence is too short. (< 5 resolved nts)
6o6x_1_D
6ywo_1_F
Sequence is too short. (< 5 resolved nts)
4ba2_1_R
6wan_1_J
Sequence is too short. (< 5 resolved nts)
7bdv_1_F
4oau_1_A
Sequence is too short. (< 5 resolved nts)
7bdv_1_H
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
Sequence is too short. (< 5 resolved nts)
6yud_1_P
Sequence is too short. (< 5 resolved nts)
6scf_1_L
Sequence is too short. (< 5 resolved nts)
6yud_1_M
Sequence is too short. (< 5 resolved nts)
6yud_1_Q
Sequence is too short. (< 5 resolved nts)
6w11_1_C
Sequence is too short. (< 5 resolved nts)
6o6x_1_D
Sequence is too short. (< 5 resolved nts)
4ba2_1_R
Sequence is too short. (< 5 resolved nts)
7bdv_1_F
Sequence is too short. (< 5 resolved nts)
7bdv_1_H
Sequence is too short. (< 5 resolved nts)
6o6x_1_C
...
...
@@ -2423,7 +2597,7 @@ 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 +2605,9 @@ 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 +2620,7 @@ 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
...
...
@@ -2482,30 +2659,9 @@ 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 +2692,15 @@ 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)
...
...
@@ -2602,11 +2752,8 @@ 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.
...
...
@@ -2653,6 +2800,12 @@ Sequence is too short. (< 5 resolved nts)
3jbu_1_V
Could not find nucleotides of chain V 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.
4ts2_1_Y
Nucleotides not inserted !
4ts0_1_Y
Nucleotides not inserted !
1h2c_1_R
Sequence is too short. (< 5 resolved nts)
...
...
@@ -2731,6 +2884,9 @@ 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.
DSSR warning 1zc8.json: no nucleotides found. Ignoring 1zc8_1_H.
6bfb_1_Y
Nucleotides not inserted !
1zc8_1_J
DSSR warning 1zc8.json: no nucleotides found. Ignoring 1zc8_1_J.
...
...
@@ -2857,6 +3016,12 @@ Could not find nucleotides of chain BB in annotation 6z1p.json. Either there is
6z1p_1_BA
Could not find nucleotides of chain BA in annotation 6z1p.json. Either there is a problem with 6z1p mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
3p22_1_C
Nucleotides not inserted !
3p22_1_G
Nucleotides not inserted !
2uxd_1_X
Sequence is too short. (< 5 resolved nts)
...
...
@@ -2923,12 +3088,6 @@ 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)
...
...
@@ -3166,6 +3325,9 @@ Sequence is too short. (< 5 resolved nts)
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.
4jf2_1_A
Nucleotides not inserted !
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.
...
...
@@ -3244,11 +3391,11 @@ 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.
3fu2_1_B
Nucleotides not inserted !
2agn_1_D
DSSR warning 2agn.json: no nucleotides found. Ignoring 2agn_1_D.
3fu2_1_A
Nucleotides not inserted !
4v5z_1_BD
DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_BD.
...
...
@@ -3355,6 +3502,39 @@ Sequence is too short. (< 5 resolved nts)
5dto_1_B
Sequence is too short. (< 5 resolved nts)
6yml_1_A
Nucleotides not inserted !
6ymm_1_A
Nucleotides not inserted !
6ymi_1_M
Nucleotides not inserted !
6ymi_1_F
Nucleotides not inserted !
6ymi_1_A
Nucleotides not inserted !
6ylb_1_F
Nucleotides not inserted !
6ymi_1_C
Nucleotides not inserted !
6ymj_1_C
Nucleotides not inserted !
6ylb_1_C
Nucleotides not inserted !
6ymj_1_I
Nucleotides not inserted !
6ymj_1_O
Nucleotides not inserted !
4cxh_1_X
Could not find nucleotides of chain X 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.
...
...
@@ -3463,6 +3643,24 @@ 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.
6ck5_1_A
Nucleotides not inserted !
6ck5_1_B
Nucleotides not inserted !
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.
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.
2vaz_1_A
DSSR warning 2vaz.json: no nucleotides found. Ignoring 2vaz_1_A.
...
...
@@ -3535,6 +3739,9 @@ Sequence is too short. (< 5 resolved nts)
5uh9_1_I
Sequence is too short. (< 5 resolved nts)
4v5z_1_BS
DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_BS.
2ftc_1_R
DSSR warning 2ftc.json: no nucleotides found. Ignoring 2ftc_1_R.
...
...
@@ -3547,9 +3754,6 @@ 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)
...
...
@@ -3631,8 +3835,8 @@ 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.
5u34_1_B
Nucleotides not inserted !
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 +3904,21 @@ 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)
...
...
@@ -3736,6 +3949,15 @@ Sequence is too short. (< 5 resolved nts)
7a5g_1_J
Could not find nucleotides of chain J in annotation 7a5g.json. Either there is a problem with 7a5g mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
1m5k_1_B
Nucleotides not inserted !
1m5o_1_E
Nucleotides not inserted !
1m5v_1_B
Nucleotides not inserted !
6gx6_1_B
Sequence is too short. (< 5 resolved nts)
...
...
@@ -3754,9 +3976,6 @@ 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)
...
...
@@ -3826,9 +4045,15 @@ Sequence is too short. (< 5 resolved nts)
6gc5_1_G
Sequence is too short. (< 5 resolved nts)
4rne_1_C
Nucleotides not inserted !
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)
...
...
@@ -3874,6 +4099,15 @@ Could not find nucleotides of chain X in annotation 5y88.json. Either there is a
4v5z_1_BB
DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_BB.
5y85_1_D
Nucleotides not inserted !
5y85_1_B
Nucleotides not inserted !
5y87_1_D
Nucleotides not inserted !
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.
...
...
@@ -4057,9 +4291,6 @@ 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.
...
...
@@ -4072,6 +4303,9 @@ Sequence is too short. (< 5 resolved nts)
1uvi_1_E
Sequence is too short. (< 5 resolved nts)
3gs5_1_A
Nucleotides not inserted !
4m7d_1_P
Sequence is too short. (< 5 resolved nts)
...
...
@@ -4132,12 +4366,12 @@ Could not find nucleotides of chain 2M in annotation 6ip6.json. Either there is
6qcs_1_M
Sequence is too short. (< 5 resolved nts)
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.
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.
...
...
@@ -4177,6 +4411,9 @@ 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.
...
...
@@ -4189,9 +4426,6 @@ 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.
...
...
@@ -4315,12 +4549,6 @@ 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)
...
...
@@ -4330,15 +4558,54 @@ Sequence is too short. (< 5 resolved nts)
3iy8_1_A
DSSR warning 3iy8.json: no nucleotides found. Ignoring 3iy8_1_A.
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_G
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_H
Sequence is too short. (< 5 resolved nts)
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.
2qwy_1_C
Nucleotides not inserted !
2qwy_1_A
Nucleotides not inserted !
2qwy_1_B
Nucleotides not inserted !
4eya_1_O
Could not find nucleotides of chain O 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.
...
...
@@ -4363,12 +4630,6 @@ 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)
...
...
@@ -4495,6 +4756,9 @@ 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.
3bnp_1_B
Nucleotides not inserted !
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.
...
...
@@ -4564,6 +4828,21 @@ Sequence is too short. (< 5 resolved nts)
4wti_1_P
Sequence is too short. (< 5 resolved nts)
6dlr_1_A
Nucleotides not inserted !
6dlt_1_A
Nucleotides not inserted !
6dls_1_A
Nucleotides not inserted !
6dlq_1_A
Nucleotides not inserted !
6dnr_1_A
Nucleotides not inserted !
5l3p_1_Y
Could not find nucleotides of chain Y in annotation 5l3p.json. Either there is a problem with 5l3p mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
...
...
@@ -4573,12 +4852,36 @@ Sequence is too short. (< 5 resolved nts)
3rzo_1_R
Sequence is too short. (< 5 resolved nts)
5wlh_1_B
Nucleotides not inserted !
2f4v_1_Z
Sequence is too short. (< 5 resolved nts)
5ml7_1_B
Nucleotides not inserted !
1qln_1_R
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.
6ogy_1_M
Sequence is too short. (< 5 resolved nts)
...
...
@@ -4588,12 +4891,12 @@ Sequence is too short. (< 5 resolved nts)
6uej_1_B
Sequence is too short. (< 5 resolved nts)
7kga_1_A
Nucleotides not inserted !
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)
...
...
@@ -4720,24 +5023,12 @@ 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.
...
...
@@ -4927,120 +5218,51 @@ Sequence is too short. (< 5 resolved nts)
4ejt_1_G
Sequence is too short. (< 5 resolved nts)
6lkq_1_W
Could not find nucleotides of chain W 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.
3qsu_1_P
Sequence is too short. (< 5 resolved nts)
3qsu_1_R
Sequence is too short. (< 5 resolved nts)
2xs7_1_B
Sequence is too short. (< 5 resolved nts)
1n38_1_B
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)
1et4_1_A
Nucleotides not inserted !
6vm6_1_G
Sequence is too short. (< 5 resolved nts)
1et4_1_C
Nucleotides not inserted !
6wan_1_K
Sequence is too short. (< 5 resolved nts)
1et4_1_B
Nucleotides not inserted !
6wan_1_H
Sequence is too short. (< 5 resolved nts)
1et4_1_D
Nucleotides not inserted !
6wan_1_G
Sequence is too short. (< 5 resolved nts)
1et4_1_E
Nucleotides not inserted !
6wan_1_L
Sequence is too short. (< 5 resolved nts)
1ddy_1_C
Nucleotides not inserted !
6wan_1_I
Sequence is too short. (< 5 resolved nts)
1ddy_1_A
Nucleotides not inserted !
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)
1ddy_1_E
Nucleotides not inserted !
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)
6lkq_1_W
Could not find nucleotides of chain W 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.
3gpq_1_F
Sequence is too short. (< 5 resolved nts)
6r47_1_A
Nucleotides not inserted !
6o79_1_C
3qsu_1_P
Sequence is too short. (< 5 resolved nts)
6vm6_1_K
3qsu_1_R
Sequence is too short. (< 5 resolved nts)
6m6v_1_G
2xs7_1_B
Sequence is too short. (< 5 resolved nts)
6hyu_1_D
1n38_1_B
Sequence is too short. (< 5 resolved nts)
1laj_1_R
4qvc_1_G
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)
...
...
@@ -5065,6 +5287,9 @@ Could not find nucleotides of chain V in annotation 6ftj.json. Either there is a
6ftg_1_V
Could not find nucleotides of chain V in annotation 6ftg.json. Either there is a problem with 6ftg mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
3npn_1_A
Nucleotides not inserted !
4g0a_1_G
Sequence is too short. (< 5 resolved nts)
...
...
@@ -5080,15 +5305,6 @@ 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)
...
...
@@ -5134,69 +5350,3 @@ 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.
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.
7am2_1_R1
Sequence is too short. (< 5 resolved nts)
7k5l_1_R
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
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.
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.
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.
curseur.execute("SELECT chain_id, nt_name, alpha, beta, gamma, delta, epsilon, zeta, chi FROM nucleotide WHERE nt_name='A' OR nt_name='C' OR nt_name='G' OR nt_name='U' ;")
liste=[]
forntincurseur.fetchall():# retrieve the angle measurements and put them in a list
liste.append(nt)
angles_torsion=[]
forntinliste:
angles_deg=[]
angles_deg.append(nt[0])#chain_id
angles_deg.append(nt[1])#nt_name
foriinrange(2,9):# on all angles
angle=0
ifnt[i]==None:
angle=None
elifnt[i]<=np.pi:#if angle value <pi, positive
angle=(180/np.pi)*nt[i]
elifnp.pi<nt[i]<=2*np.pi:#if value of the angle between pi and 2pi, negative
curseur.execute("SELECT chain_id, nt_name, eta, theta, eta_prime, theta_prime, eta_base, theta_base FROM nucleotide WHERE nt_name='A' OR nt_name='C' OR nt_name='G' OR nt_name='U';")
liste=[]
forntincurseur.fetchall():
liste.append(nt)
angles_virtuels=[]
forntinliste:
angles_deg=[]
angles_deg.append(nt[0])#chain_id
angles_deg.append(nt[1])#nt_name
foriinrange(2,8):
angle=0
ifnt[i]==None:
angle=None
elifnt[i]<=np.pi:
angle=(180/np.pi)*nt[i]
elifnp.pi<nt[i]<=2*np.pi:
angle=((180/np.pi)*nt[i])-360
else:
angle=nt[i]
angles_deg.append(angle)
angles_virtuels.append(angles_deg)
returnangles_virtuels
defnt_3d_centers(cif_file,consider_all_atoms):
"""Return the nucleotides' coordinates, summarizing a nucleotide by only one point.