From 60f0af5acad06695acd782f9401f5e166852f45f Mon Sep 17 00:00:00 2001 From: Louis Becquey Date: Wed, 18 Aug 2021 09:10:30 +0200 Subject: [PATCH] Modified couple of GMM n modes --- geometric_stats.py | 12 ++++----- known_issues.txt | 22 +++++---------- known_issues_reasons.txt | 58 ++++++++++------------------------------ 3 files changed, 26 insertions(+), 66 deletions(-) diff --git a/geometric_stats.py b/geometric_stats.py index 797626b..08d6c07 100644 --- a/geometric_stats.py +++ b/geometric_stats.py @@ -55,7 +55,7 @@ "P-O5'-C5'":2, "O5'-C5'-C4'":1, "C5'-C4'-P":2, "C5'-C4'-C1'":2, "C4'-P-O5'":2, "C4'-C1'-B1":2, "C1'-C4'-P":2, "C1'-B1-B2":2, # HiRE-RNA, torsions - "P-O5'-C5'-C4'":1, "O5'-C5'-C4'-P°":3, "O5'-C5'-C4'-C1'":3, "C5'-C4'-P°-O5'°":3, "C5'-C4'-C1'-B1":2, "C4'-P°-O5'°-C5'°":3, "C4'-C1'-B1-B2":3, "C1'-C4'-P°-O5'°":3, + "P-O5'-C5'-C4'":3, "O5'-C5'-C4'-P°":3, "O5'-C5'-C4'-C1'":3, "C5'-C4'-P°-O5'°":3, "C5'-C4'-C1'-B1":2, "C4'-P°-O5'°-C5'°":3, "C4'-C1'-B1-B2":3, "C1'-C4'-P°-O5'°":3, # HiRE-RNA, basepairs "cWW_AA_tips_distance":3, "cWW_AA_C1'-B1-B1pair":1, "cWW_AA_B1-B1pair-C1'pair":1, "cWW_AA_C4'-C1'-B1-B1pair":2, "cWW_AA_B1-B1pair-C1'pair-C4'pair":3, "cWW_AA_alpha_1":2, "cWW_AA_alpha_2":3, "cWW_AA_dB1":3, "cWW_AA_dB2":3, @@ -172,7 +172,7 @@ "tWH_CG_tips_distance":4, "tWH_CG_C1'-B1-B1pair":2, "tWH_CG_B1-B1pair-C1'pair":1, "tWH_CG_C4'-C1'-B1-B1pair":2, "tWH_CG_B1-B1pair-C1'pair-C4'pair":3, "tWH_CG_alpha_1":2, "tWH_CG_alpha_2":1, "tWH_CG_dB1":3, "tWH_CG_dB2":2, "cHW_CG_tips_distance":3, "cHW_CG_C1'-B1-B1pair":2, "cHW_CG_B1-B1pair-C1'pair":2, "cHW_CG_C4'-C1'-B1-B1pair":1, "cHW_CG_B1-B1pair-C1'pair-C4'pair":2, "cHW_CG_alpha_1":1, "cHW_CG_alpha_2":2, "cHW_CG_dB1":2, "cHW_CG_dB2":2, "tHW_CG_tips_distance":5, "tHW_CG_C1'-B1-B1pair":1, "tHW_CG_B1-B1pair-C1'pair":2, "tHW_CG_C4'-C1'-B1-B1pair":1, "tHW_CG_B1-B1pair-C1'pair-C4'pair":2, "tHW_CG_alpha_1":3, "tHW_CG_alpha_2":2, "tHW_CG_dB1":4, "tHW_CG_dB2":3, - "cWS_CG_tips_distance":2, "cWS_CG_C1'-B1-B1pair":1, "cWS_CG_B1-B1pair-C1'pair":1, "cWS_CG_C4'-C1'-B1-B1pair":1, "cWS_CG_B1-B1pair-C1'pair-C4'pair":1, "cWS_CG_alpha_1":1, "cWS_CG_alpha_2":2, "cWS_CG_dB1":2, "cWS_CG_dB2":3, + "cWS_CG_tips_distance":2, "cWS_CG_C1'-B1-B1pair":1, "cWS_CG_B1-B1pair-C1'pair":1, "cWS_CG_C4'-C1'-B1-B1pair":2, "cWS_CG_B1-B1pair-C1'pair-C4'pair":1, "cWS_CG_alpha_1":1, "cWS_CG_alpha_2":2, "cWS_CG_dB1":2, "cWS_CG_dB2":3, "tWS_CG_tips_distance":2, "tWS_CG_C1'-B1-B1pair":3, "tWS_CG_B1-B1pair-C1'pair":1, "tWS_CG_C4'-C1'-B1-B1pair":2, "tWS_CG_B1-B1pair-C1'pair-C4'pair":1, "tWS_CG_alpha_1":2, "tWS_CG_alpha_2":1, "tWS_CG_dB1":2, "tWS_CG_dB2":4, "cSW_CG_tips_distance":7, "cSW_CG_C1'-B1-B1pair":1, "cSW_CG_B1-B1pair-C1'pair":2, "cSW_CG_C4'-C1'-B1-B1pair":2, "cSW_CG_B1-B1pair-C1'pair-C4'pair":3, "cSW_CG_alpha_1":1, "cSW_CG_alpha_2":2, "cSW_CG_dB1":1, "cSW_CG_dB2":3, "tSW_CG_tips_distance":4, "tSW_CG_C1'-B1-B1pair":1, "tSW_CG_B1-B1pair-C1'pair":2, "tSW_CG_C4'-C1'-B1-B1pair":3, "tSW_CG_B1-B1pair-C1'pair-C4'pair":2, "tSW_CG_alpha_1":1, "tSW_CG_alpha_2":2, "tSW_CG_dB1":7, "tSW_CG_dB2":2, @@ -190,7 +190,7 @@ "tWH_CU_tips_distance":1, "tWH_CU_C1'-B1-B1pair":2, "tWH_CU_B1-B1pair-C1'pair":2, "tWH_CU_C4'-C1'-B1-B1pair":3, "tWH_CU_B1-B1pair-C1'pair-C4'pair":2, "tWH_CU_alpha_1":3, "tWH_CU_alpha_2":3, "tWH_CU_dB1":5, "tWH_CU_dB2":2, "cHW_CU_tips_distance":3, "cHW_CU_C1'-B1-B1pair":2, "cHW_CU_B1-B1pair-C1'pair":2, "cHW_CU_C4'-C1'-B1-B1pair":1, "cHW_CU_B1-B1pair-C1'pair-C4'pair":3, "cHW_CU_alpha_1":2, "cHW_CU_alpha_2":2, "cHW_CU_dB1":1, "cHW_CU_dB2":3, "tHW_CU_tips_distance":8, "tHW_CU_C1'-B1-B1pair":1, "tHW_CU_B1-B1pair-C1'pair":1, "tHW_CU_C4'-C1'-B1-B1pair":3, "tHW_CU_B1-B1pair-C1'pair-C4'pair":2, "tHW_CU_alpha_1":1, "tHW_CU_alpha_2":2, "tHW_CU_dB1":3, "tHW_CU_dB2":3, - "cWS_CU_tips_distance":4, "cWS_CU_C1'-B1-B1pair":1, "cWS_CU_B1-B1pair-C1'pair":2, "cWS_CU_C4'-C1'-B1-B1pair":2, "cWS_CU_B1-B1pair-C1'pair-C4'pair":2, "cWS_CU_alpha_1":3, "cWS_CU_alpha_2":2, "cWS_CU_dB1":4, "cWS_CU_dB2":2, + "cWS_CU_tips_distance":4, "cWS_CU_C1'-B1-B1pair":1, "cWS_CU_B1-B1pair-C1'pair":2, "cWS_CU_C4'-C1'-B1-B1pair":3, "cWS_CU_B1-B1pair-C1'pair-C4'pair":2, "cWS_CU_alpha_1":3, "cWS_CU_alpha_2":2, "cWS_CU_dB1":4, "cWS_CU_dB2":2, "tWS_CU_tips_distance":5, "tWS_CU_C1'-B1-B1pair":3, "tWS_CU_B1-B1pair-C1'pair":1, "tWS_CU_C4'-C1'-B1-B1pair":2, "tWS_CU_B1-B1pair-C1'pair-C4'pair":2, "tWS_CU_alpha_1":2, "tWS_CU_alpha_2":1, "tWS_CU_dB1":3, "tWS_CU_dB2":5, "cSW_CU_tips_distance":3, "cSW_CU_C1'-B1-B1pair":2, "cSW_CU_B1-B1pair-C1'pair":2, "cSW_CU_C4'-C1'-B1-B1pair":2, "cSW_CU_B1-B1pair-C1'pair-C4'pair":3, "cSW_CU_alpha_1":3, "cSW_CU_alpha_2":3, "cSW_CU_dB1":2, "cSW_CU_dB2":4, "tSW_CU_tips_distance":7, "tSW_CU_C1'-B1-B1pair":2, "tSW_CU_B1-B1pair-C1'pair":2, "tSW_CU_C4'-C1'-B1-B1pair":2, "tSW_CU_B1-B1pair-C1'pair-C4'pair":2, "tSW_CU_alpha_1":2, "tSW_CU_alpha_2":2, "tSW_CU_dB1":2, "tSW_CU_dB2":2, @@ -203,7 +203,7 @@ "cSS_CU_tips_distance":5, "cSS_CU_C1'-B1-B1pair":2, "cSS_CU_B1-B1pair-C1'pair":2, "cSS_CU_C4'-C1'-B1-B1pair":1, "cSS_CU_B1-B1pair-C1'pair-C4'pair":1, "cSS_CU_alpha_1":2, "cSS_CU_alpha_2":3, "cSS_CU_dB1":6, "cSS_CU_dB2":1, "tSS_CU_tips_distance":5, "tSS_CU_C1'-B1-B1pair":2, "tSS_CU_B1-B1pair-C1'pair":3, "tSS_CU_C4'-C1'-B1-B1pair":2, "tSS_CU_B1-B1pair-C1'pair-C4'pair":2, "tSS_CU_alpha_1":3, "tSS_CU_alpha_2":3, "tSS_CU_dB1":7, "tSS_CU_dB2":2, "cWW_GA_tips_distance":5, "cWW_GA_C1'-B1-B1pair":1, "cWW_GA_B1-B1pair-C1'pair":1, "cWW_GA_C4'-C1'-B1-B1pair":2, "cWW_GA_B1-B1pair-C1'pair-C4'pair":2, "cWW_GA_alpha_1":1, "cWW_GA_alpha_2":1, "cWW_GA_dB1":2, "cWW_GA_dB2":1, - "tWW_GA_tips_distance":6, "tWW_GA_C1'-B1-B1pair":1, "tWW_GA_B1-B1pair-C1'pair":1, "tWW_GA_C4'-C1'-B1-B1pair":1, "tWW_GA_B1-B1pair-C1'pair-C4'pair":2, "tWW_GA_alpha_1":1, "tWW_GA_alpha_2":2, "tWW_GA_dB1":1, "tWW_GA_dB2":2, + "tWW_GA_tips_distance":6, "tWW_GA_C1'-B1-B1pair":1, "tWW_GA_B1-B1pair-C1'pair":1, "tWW_GA_C4'-C1'-B1-B1pair":1, "tWW_GA_B1-B1pair-C1'pair-C4'pair":2, "tWW_GA_alpha_1":2, "tWW_GA_alpha_2":2, "tWW_GA_dB1":1, "tWW_GA_dB2":2, "cWH_GA_tips_distance":2, "cWH_GA_C1'-B1-B1pair":1, "cWH_GA_B1-B1pair-C1'pair":1, "cWH_GA_C4'-C1'-B1-B1pair":3, "cWH_GA_B1-B1pair-C1'pair-C4'pair":2, "cWH_GA_alpha_1":2, "cWH_GA_alpha_2":1, "cWH_GA_dB1":2, "cWH_GA_dB2":2, "tWH_GA_tips_distance":7, "tWH_GA_C1'-B1-B1pair":1, "tWH_GA_B1-B1pair-C1'pair":2, "tWH_GA_C4'-C1'-B1-B1pair":1, "tWH_GA_B1-B1pair-C1'pair-C4'pair":2, "tWH_GA_alpha_1":2, "tWH_GA_alpha_2":2, "tWH_GA_dB1":1, "tWH_GA_dB2":6, "cHW_GA_tips_distance":4, "cHW_GA_C1'-B1-B1pair":2, "cHW_GA_B1-B1pair-C1'pair":2, "cHW_GA_C4'-C1'-B1-B1pair":2, "cHW_GA_B1-B1pair-C1'pair-C4'pair":3, "cHW_GA_alpha_1":1, "cHW_GA_alpha_2":2, "cHW_GA_dB1":1, "cHW_GA_dB2":4, @@ -227,7 +227,7 @@ "cHW_GC_tips_distance":4, "cHW_GC_C1'-B1-B1pair":1, "cHW_GC_B1-B1pair-C1'pair":1, "cHW_GC_C4'-C1'-B1-B1pair":2, "cHW_GC_B1-B1pair-C1'pair-C4'pair":2, "cHW_GC_alpha_1":1, "cHW_GC_alpha_2":1, "cHW_GC_dB1":3, "cHW_GC_dB2":4, "tHW_GC_tips_distance":5, "tHW_GC_C1'-B1-B1pair":2, "tHW_GC_B1-B1pair-C1'pair":2, "tHW_GC_C4'-C1'-B1-B1pair":2, "tHW_GC_B1-B1pair-C1'pair-C4'pair":2, "tHW_GC_alpha_1":2, "tHW_GC_alpha_2":2, "tHW_GC_dB1":2, "tHW_GC_dB2":4, "cWS_GC_tips_distance":8, "cWS_GC_C1'-B1-B1pair":1, "cWS_GC_B1-B1pair-C1'pair":1, "cWS_GC_C4'-C1'-B1-B1pair":2, "cWS_GC_B1-B1pair-C1'pair-C4'pair":2, "cWS_GC_alpha_1":2, "cWS_GC_alpha_2":1, "cWS_GC_dB1":2, "cWS_GC_dB2":1, - "tWS_GC_tips_distance":2, "tWS_GC_C1'-B1-B1pair":1, "tWS_GC_B1-B1pair-C1'pair":1, "tWS_GC_C4'-C1'-B1-B1pair":3, "tWS_GC_B1-B1pair-C1'pair-C4'pair":2, "tWS_GC_alpha_1":1, "tWS_GC_alpha_2":1, "tWS_GC_dB1":4, "tWS_GC_dB2":5, + "tWS_GC_tips_distance":2, "tWS_GC_C1'-B1-B1pair":1, "tWS_GC_B1-B1pair-C1'pair":1, "tWS_GC_C4'-C1'-B1-B1pair":3, "tWS_GC_B1-B1pair-C1'pair-C4'pair":2, "tWS_GC_alpha_1":2, "tWS_GC_alpha_2":1, "tWS_GC_dB1":4, "tWS_GC_dB2":5, "cSW_GC_tips_distance":4, "cSW_GC_C1'-B1-B1pair":2, "cSW_GC_B1-B1pair-C1'pair":3, "cSW_GC_C4'-C1'-B1-B1pair":1, "cSW_GC_B1-B1pair-C1'pair-C4'pair":2, "cSW_GC_alpha_1":3, "cSW_GC_alpha_2":2, "cSW_GC_dB1":3, "cSW_GC_dB2":2, "tSW_GC_tips_distance":2, "tSW_GC_C1'-B1-B1pair":1, "tSW_GC_B1-B1pair-C1'pair":3, "tSW_GC_C4'-C1'-B1-B1pair":1, "tSW_GC_B1-B1pair-C1'pair-C4'pair":2, "tSW_GC_alpha_1":2, "tSW_GC_alpha_2":2, "tSW_GC_dB1":4, "tSW_GC_dB2":2, "cHH_GC_tips_distance":1, "cHH_GC_C1'-B1-B1pair":3, "cHH_GC_B1-B1pair-C1'pair":1, "cHH_GC_C4'-C1'-B1-B1pair":2, "cHH_GC_B1-B1pair-C1'pair-C4'pair":1, "cHH_GC_alpha_1":2, "cHH_GC_alpha_2":2, "cHH_GC_dB1":3, "cHH_GC_dB2":3, @@ -1884,7 +1884,7 @@ def concat_jsons(flist, outfilename): result = [] for f in flist: if not os.path.isfile(f): - warn("Unable to find "+f) + warn("Unable to find "+f.split('/')[-1]) continue with open(f, "rb") as infile: result.append(json.load(infile)) diff --git a/known_issues.txt b/known_issues.txt index b06dc5c..fb98a58 100644 --- a/known_issues.txt +++ b/known_issues.txt @@ -723,7 +723,6 @@ 6r7b_1_E 6o7i_1_I 6o7h_1_K -7a5g_1_A3 7l6t_1_C 7jyy_1_F 7jyy_1_E @@ -816,7 +815,6 @@ 6ppn_1_A 6ppn_1_I 5flx_1_Z -7a5g_1_B3 6eri_1_AX 7k5l_1_R 7d80_1_Y @@ -853,7 +851,6 @@ 4x9e_1_H 6z1p_1_BB 6z1p_1_BA -7a5g_1_A6 2uxd_1_X 6ywe_1_BB 3ol9_1_D @@ -1053,8 +1050,6 @@ 6l74_1_I 5uh9_1_I 7a5j_1_X -7a5g_1_24 -7a5g_1_C 6sag_1_R 4udv_1_R 5zsc_1_D @@ -1518,25 +1513,20 @@ 7d0g_1_A_805-913 7d0f_1_A_817-913 7o7z_1_AH_144-220 -7a5g_1_A3_1-1454 -7a5g_1_A6_4-949 4c9d_1_D_29-1 4c9d_1_C_29-1 -7a5g_1_24_1-70 -7a5g_1_C_1-70 -7a5g_1_j_1-73 -7aih_1_1_2984-3610 7aih_1_1_2400-2963 -7ane_1_2_2489-3115 +7aih_1_1_2984-3610 7ane_1_2_1904-2468 +7ane_1_2_2489-3115 5g2x_1_A_595-692 -7aor_1_2_2589-3210 7aor_1_2_2020-2579 +7aor_1_2_2589-3210 7a5p_1_2_259-449 -7aor_1_A_2589-3210 7aor_1_A_2020-2579 -7am2_1_1_2491-3117 +7aor_1_A_2589-3210 7am2_1_1_1904-2470 -7ane_1_1_2489-3115 +7am2_1_1_2491-3117 7ane_1_1_1904-2468 +7ane_1_1_2489-3115 6uz7_1_8_2140-2825 diff --git a/known_issues_reasons.txt b/known_issues_reasons.txt index 4d3c0a2..4f608f5 100644 --- a/known_issues_reasons.txt +++ b/known_issues_reasons.txt @@ -1145,7 +1145,7 @@ Could not find nucleotides of chain U3 in annotation 7a5k.json. Either there is Could not find nucleotides of chain U in annotation 6nu2.json. Either there is a problem with 6nu2 mmCIF download, or the bases are not resolved in the structure. Delete it and retry. 7a5g_1_U3 -Could not download and/or find annotations for 7a5g_1_U3. +Could not find nucleotides of chain U3 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. 6nu3_1_U Could not find nucleotides of chain U in annotation 6nu3.json. Either there is a problem with 6nu3 mmCIF download, or the bases are not resolved in the structure. Delete it and retry. @@ -2173,9 +2173,6 @@ Sequence is too short. (< 5 resolved nts) 6o7h_1_K Sequence is too short. (< 5 resolved nts) -7a5g_1_A3 -Could not download and/or find annotations for 7a5g_1_A3. - 7l6t_1_C Sequence is too short. (< 5 resolved nts) @@ -2452,9 +2449,6 @@ Sequence is too short. (< 5 resolved nts) 5flx_1_Z Could not find nucleotides of chain Z in annotation 5flx.json. Either there is a problem with 5flx mmCIF download, or the bases are not resolved in the structure. Delete it and retry. -7a5g_1_B3 -Could not download and/or find annotations for 7a5g_1_B3. - 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. @@ -2563,9 +2557,6 @@ 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. -7a5g_1_A6 -Could not download and/or find annotations for 7a5g_1_A6. - 2uxd_1_X Sequence is too short. (< 5 resolved nts) @@ -3163,12 +3154,6 @@ Sequence is too short. (< 5 resolved nts) 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. -7a5g_1_24 -Could not download and/or find annotations for 7a5g_1_24. - -7a5g_1_C -Could not download and/or find annotations for 7a5g_1_C. - 6sag_1_R Sequence is too short. (< 5 resolved nts) @@ -3365,7 +3350,7 @@ Sequence is too short. (< 5 resolved nts) Sequence is too short. (< 5 resolved nts) 7a5g_1_J -Could not download and/or find annotations for 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. 6gx6_1_B Sequence is too short. (< 5 resolved nts) @@ -4558,67 +4543,52 @@ Could not find nucleotides of chain A in annotation 7d0f.json. Either there is a 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. -7a5g_1_A3_1-1454 -Could not download and/or find annotations for 7a5g_1_A3_1-1454. - -7a5g_1_A6_4-949 -Could not download and/or find annotations for 7a5g_1_A6_4-949. - 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). -7a5g_1_24_1-70 -Could not download and/or find annotations for 7a5g_1_24_1-70. - -7a5g_1_C_1-70 -Could not download and/or find annotations for 7a5g_1_C_1-70. - -7a5g_1_j_1-73 -Could not download and/or find annotations for 7a5g_1_j_1-73. - -7aih_1_1_2984-3610 +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. -7aih_1_1_2400-2963 +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. -7ane_1_2_2489-3115 +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. -7ane_1_2_1904-2468 +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. 5g2x_1_A_595-692 Sequence is too short. (< 5 resolved nts) -7aor_1_2_2589-3210 +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. -7aor_1_2_2020-2579 +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. 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. -7aor_1_A_2589-3210 +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. -7aor_1_A_2020-2579 +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_2491-3117 +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_1904-2470 +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_2489-3115 +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_1904-2468 +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