id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3731 residue_graph: edges should be a n x 2 array of unsigned ints sitins07@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19041 ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > X:/Work/Projects/48S/Modelling/Closed/48S_closed_cut_real_space_refined- > coot-0.pdb X:/Work/Projects/48S/Modelling/Closed/360_closed_37A.mrc Summary of feedback from opening X:/Work/Projects/48S/Modelling/Closed/48S_closed_cut_real_space_refined- coot-0.pdb --- warning | Ignored bad PDB record found on line 118332 END Chain information for 48S_closed_cut_real_space_refined-coot-0.pdb #1 --- Chain | Description 1 | No description available 2 | No description available 3 | No description available 4 | No description available 5 | No description available 6 | No description available 7 | No description available 8 | No description available A | No description available B | No description available C | No description available D | No description available E | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available Q | No description available R | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c | No description available e | No description available f | No description available g | No description available h | No description available i | No description available j | No description available k | No description available l | No description available n | No description available o | No description available q | No description available r | No description available s | No description available t | No description available u | No description available v | No description available w | No description available Opened 360_closed_37A.mrc, grid size 360,360,360, pixel 1.16, shown at level 4.12, step 2, values float32 > volume #2 step 1 > style stick Changed 117622 atom styles > ui tool show ISOLDE > set selectionWidth 4 Chain information for 48S_closed_cut_real_space_refined-coot-0.pdb --- Chain | Description 1.2/1 | No description available 1.2/2 | No description available 1.2/3 | No description available 1.2/4 | No description available 1.2/5 | No description available 1.2/6 | No description available 1.2/7 | No description available 1.2/8 | No description available 1.2/A | No description available 1.2/B | No description available 1.2/C | No description available 1.2/D | No description available 1.2/E | No description available 1.2/G | No description available 1.2/H | No description available 1.2/I | No description available 1.2/J | No description available 1.2/K | No description available 1.2/L | No description available 1.2/M | No description available 1.2/N | No description available 1.2/O | No description available 1.2/Q | No description available 1.2/R | No description available 1.2/T | No description available 1.2/U | No description available 1.2/V | No description available 1.2/W | No description available 1.2/X | No description available 1.2/Y | No description available 1.2/Z | No description available 1.2/a | No description available 1.2/b | No description available 1.2/c | No description available 1.2/e | No description available 1.2/f | No description available 1.2/g | No description available 1.2/h | No description available 1.2/i | No description available 1.2/j | No description available 1.2/k | No description available 1.2/l | No description available 1.2/n | No description available 1.2/o | No description available 1.2/q | No description available 1.2/r | No description available 1.2/s | No description available 1.2/t | No description available 1.2/u | No description available 1.2/v | No description available 1.2/w | No description available Done loading forcefield > volume #1.1.1.1 level 7.775 > addh Summary of feedback from adding hydrogens to 48S_closed_cut_real_space_refined-coot-0.pdb #1.2 --- warnings | Not adding hydrogens to /1 LYS 606 N because it is missing heavy- atom bond partners Not adding hydrogens to /2 TYR 577 CB because it is missing heavy-atom bond partners Not adding hydrogens to /2 LYS 877 N because it is missing heavy-atom bond partners Not adding hydrogens to /3 GLU 423 N because it is missing heavy-atom bond partners Not adding hydrogens to /6 SER 217 N because it is missing heavy-atom bond partners 2 messages similar to the above omitted The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: /3 GLU 423 N; /6 SER 217 N; /7 LEU 553 N; /2 LYS 877 N; /1 LYS 606 N; /8 LEU 371 N notes | No usable SEQRES records for 48S_closed_cut_real_space_refined- coot-0.pdb (#1.2) chain 1; guessing termini instead No usable SEQRES records for 48S_closed_cut_real_space_refined-coot-0.pdb (#1.2) chain 2; guessing termini instead No usable SEQRES records for 48S_closed_cut_real_space_refined-coot-0.pdb (#1.2) chain 3; guessing termini instead No usable SEQRES records for 48S_closed_cut_real_space_refined-coot-0.pdb (#1.2) chain 4; guessing termini instead No usable SEQRES records for 48S_closed_cut_real_space_refined-coot-0.pdb (#1.2) chain 5; guessing termini instead 46 messages similar to the above omitted Chain-initial residues that are actual N termini: /1 ARG 7, /2 LYS 320, /3 TYR 4, /4 PHE 106, /5 GLY 29, /6 ALA 2, /7 GLN 181, /8 PHE 6, /A U 1, /B THR 2, /C LYS 82, /D SER 172, /E GLN 52, /G MET 1, /H PRO 6, /I MET 1, /J GLN 4, /K TRP 7, /L PRO 6, /M SER 3, /N A 1, /O CYS 6, /Q MET 1, /R VAL 4, /T LYS 23, /U THR 14, /V LYS 75, /W ARG 41, /X SER 5, /Y MET 1, /Z GLY 2, /a VAL 2, /b MET 1, /c GLY 38, /e MET 1, /f SER 2, /g MET 1, /h ALA 16, /i LYS 19, /j SER 16, /k THR 2, /l ARG 5, /n VAL 4, /o GLY 2, /q MET 1, /r GLY 9, /s ASP 3, /t MET 1, /u TYR 1, /v C 3, /w GLN 208 Chain-initial residues that are not actual N termini: /A G 267, /A G 683, /A C 730, /A C 744, /A U 774, /D GLY 361, /D THR 398 Chain-final residues that are actual C termini: /1 LYS 606, /2 LYS 877, /3 GLU 423, /4 LEU 377, /5 ASN 352, /6 SER 217, /7 LEU 553, /8 LEU 371, /A A 1863, /B ILE 314, /C LYS 152, /E ARG 473, /G PHE 158, /H ARG 146, /I GLY 263, /J ASP 56, /K GLY 188, /L ARG 142, /M PRO 19, /N A 75, /O VAL 271, /Q ARG 142, /R LYS 144, /U ARG 204, /V SER 133, /W GLY 115, /X LEU 194, /Y HIS 84, /Z ALA 151, /a PHE 130, /b ASN 82, /c THR 263, /e MET 126, /f GLU 209, /g LYS 227, /h ALA 119, /i GLY 233, /j LEU 151, /k ARG 100, /l LEU 68, /n ARG 130, /o GLY 207, /q LEU 237, /r LYS 132, /s GLU 133, /t ARG 98, /v U 28 Chain-final residues that are not actual C termini: /A C 243, /A U 679, /A G 687, /A C 736, /A G 761, /D THR 536, /D ILE 355, /D GLY 393, /T GLU 128, /u ALA 76, /w ARG 610 10107 hydrogen bonds Adding 'H' to /D GLY 361 Adding 'H' to /D THR 398 /D THR 536 is not terminus, removing H atom from 'C' /D ILE 355 is not terminus, removing H atom from 'C' /D GLY 393 is not terminus, removing H atom from 'C' /T GLU 128 is not terminus, removing H atom from 'C' /u ALA 76 is not terminus, removing H atom from 'C' 1 messages similar to the above omitted 99866 hydrogens added Fetching CCD LYS_LL from http://ligand- expo.rcsb.org/reports/L/LYS_LL/LYS_LL.cif Traceback (most recent call last): File ""C:\Users\Valentyn\AppData\Local\UCSF\ChimeraX\1.0\site- packages\chimerax\isolde\validation\unparameterised.py"", line 183, in _fix_selected_unparameterised_residue fix_residue_to_match_md_template(self.session, r, template, cif_template=ccd_template) File ""C:\Users\Valentyn\AppData\Local\UCSF\ChimeraX\1.0\site- packages\chimerax\isolde\atomic\template_utils.py"", line 324, in fix_residue_to_match_md_template fix_residue_from_template(residue, cif_template, template_indices=ccd_indices) File ""C:\Users\Valentyn\AppData\Local\UCSF\ChimeraX\1.0\site- packages\chimerax\isolde\atomic\template_utils.py"", line 198, in fix_residue_from_template matched_nodes, residue_extra, template_extra = find_maximal_isomorphous_fragment(residue, template, limit_template_indices=template_indices, match_by=match_by) File ""C:\Users\Valentyn\AppData\Local\UCSF\ChimeraX\1.0\site- packages\chimerax\isolde\atomic\template_utils.py"", line 153, in find_maximal_isomorphous_fragment rg = residue_graph(residue, label=match_by) File ""C:\Users\Valentyn\AppData\Local\UCSF\ChimeraX\1.0\site- packages\chimerax\isolde\atomic\template_utils.py"", line 99, in residue_graph return make_graph_from_residue(residue, label=label) File ""C:\Users\Valentyn\AppData\Local\UCSF\ChimeraX\1.0\site- packages\chimerax\isolde\graph\\__init__.py"", line 26, in make_graph_from_residue return Graph(labels, edges) RuntimeError: edges should be a n x 2 array of unsigned ints! RuntimeError: edges should be a n x 2 array of unsigned ints! File ""C:\Users\Valentyn\AppData\Local\UCSF\ChimeraX\1.0\site- packages\chimerax\isolde\graph\\__init__.py"", line 26, in make_graph_from_residue return Graph(labels, edges) See log for complete Python traceback. Traceback (most recent call last): File ""C:\Users\Valentyn\AppData\Local\UCSF\ChimeraX\1.0\site- packages\chimerax\isolde\validation\unparameterised.py"", line 183, in _fix_selected_unparameterised_residue fix_residue_to_match_md_template(self.session, r, template, cif_template=ccd_template) File ""C:\Users\Valentyn\AppData\Local\UCSF\ChimeraX\1.0\site- packages\chimerax\isolde\atomic\template_utils.py"", line 324, in fix_residue_to_match_md_template fix_residue_from_template(residue, cif_template, template_indices=ccd_indices) File ""C:\Users\Valentyn\AppData\Local\UCSF\ChimeraX\1.0\site- packages\chimerax\isolde\atomic\template_utils.py"", line 198, in fix_residue_from_template matched_nodes, residue_extra, template_extra = find_maximal_isomorphous_fragment(residue, template, limit_template_indices=template_indices, match_by=match_by) File ""C:\Users\Valentyn\AppData\Local\UCSF\ChimeraX\1.0\site- packages\chimerax\isolde\atomic\template_utils.py"", line 153, in find_maximal_isomorphous_fragment rg = residue_graph(residue, label=match_by) File ""C:\Users\Valentyn\AppData\Local\UCSF\ChimeraX\1.0\site- packages\chimerax\isolde\atomic\template_utils.py"", line 99, in residue_graph return make_graph_from_residue(residue, label=label) File ""C:\Users\Valentyn\AppData\Local\UCSF\ChimeraX\1.0\site- packages\chimerax\isolde\graph\\__init__.py"", line 26, in make_graph_from_residue return Graph(labels, edges) RuntimeError: edges should be a n x 2 array of unsigned ints! RuntimeError: edges should be a n x 2 array of unsigned ints! File ""C:\Users\Valentyn\AppData\Local\UCSF\ChimeraX\1.0\site- packages\chimerax\isolde\graph\\__init__.py"", line 26, in make_graph_from_residue return Graph(labels, edges) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 452.06 OpenGL renderer: GeForce GTX 1070/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Micro-Star International Co., Ltd. Model: GE73VR 7RF OS: Майкрософт Windows 10 Pro (Build 19041) Memory: 17,059,950,592 MaxProcessMemory: 137,438,953,344 CPU: 8 Intel(R) Core(TM) i7-7700HQ CPU @ 2.80GHz"" PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.8 }}} " defect assigned normal Third Party all ChimeraX