id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3523 open .pdbqt: list index out of range santiago.jus.are@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.18362 ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC) Description We were not able to open a .pdbqt file generated by autodock vina 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 > ui tool show ViewDockX No suitable models found for ViewDockX > open cadambine_out.pdbqt No such file/path: cadambine_out.pdbqt > open C:\Users\Santiago\Escritorio\DOCK\cadambine_out.pdbqt Summary of feedback from opening C:\Users\Santiago\Escritorio\DOCK\cadambine_out.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -7.9 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 9 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C17_29 and O3_3 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C8_20 and O3_3 292 messages similar to the above omitted Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 258, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 101, in cmd_open Command(session, registry=registry).run(provider_cmd_text, log=log) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 152, in provider_open name or model_name_from_path(fi.file_name)), provider_kw) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 382, in collated_open return func(*func_args, **func_kw) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\viewdockx\\__init__.py"", line 56, in open return opener(session, data, file_name, True, True) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\viewdockx\pdbqt.py"", line 6, in open_pdbqt _extract_metadata(session, f, structures) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\viewdockx\pdbqt.py"", line 34, in _extract_metadata structures[model_index].viewdockx_data = vina_values IndexError: list index out of range IndexError: list index out of range File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\viewdockx\pdbqt.py"", line 34, in _extract_metadata structures[model_index].viewdockx_data = vina_values See log for complete Python traceback. > ui tool show ViewDockX No suitable models found for ViewDockX > open C:\Users\Santiago\Escritorio\DOCK\cadambine.pdbqt Summary of feedback from opening C:\Users\Santiago\Escritorio\DOCK\cadambine.pdbqt --- warnings | Ignored bad PDB record found on line 1 REMARK 9 active torsions: Ignored bad PDB record found on line 2 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 3 REMARK 1 A between atoms: C17_29 and O3_3 Ignored bad PDB record found on line 4 REMARK 2 A between atoms: C8_20 and O3_3 Ignored bad PDB record found on line 5 REMARK 3 A between atoms: C16_28 and O5_5 27 messages similar to the above omitted Opened cadambine.pdbqt containing 1 structures (44 atoms, 50 bonds) > open C:\Users\Santiago\Escritorio\DOCK\cadambine_out.pdbqt Summary of feedback from opening C:\Users\Santiago\Escritorio\DOCK\cadambine_out.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -7.9 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 9 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C17_29 and O3_3 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C8_20 and O3_3 292 messages similar to the above omitted Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 258, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 101, in cmd_open Command(session, registry=registry).run(provider_cmd_text, log=log) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 152, in provider_open name or model_name_from_path(fi.file_name)), provider_kw) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 382, in collated_open return func(*func_args, **func_kw) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\viewdockx\\__init__.py"", line 56, in open return opener(session, data, file_name, True, True) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\viewdockx\pdbqt.py"", line 6, in open_pdbqt _extract_metadata(session, f, structures) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\viewdockx\pdbqt.py"", line 34, in _extract_metadata structures[model_index].viewdockx_data = vina_values IndexError: list index out of range IndexError: list index out of range File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\viewdockx\pdbqt.py"", line 34, in _extract_metadata structures[model_index].viewdockx_data = vina_values See log for complete Python traceback. > open C:\Users\Santiago\Escritorio\DOCK\clpro.pdbqt Chain information for clpro.pdbqt #2 --- Chain | Description A | No description available B | No description available Opened clpro.pdbqt containing 1 structures (5809 atoms, 5918 bonds) > open C:\Users\Santiago\Escritorio\DOCK\cadambine_out.pdbqt Summary of feedback from opening C:\Users\Santiago\Escritorio\DOCK\cadambine_out.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -7.9 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 9 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C17_29 and O3_3 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C8_20 and O3_3 292 messages similar to the above omitted Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 258, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 101, in cmd_open Command(session, registry=registry).run(provider_cmd_text, log=log) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 152, in provider_open name or model_name_from_path(fi.file_name)), provider_kw) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 382, in collated_open return func(*func_args, **func_kw) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\viewdockx\\__init__.py"", line 56, in open return opener(session, data, file_name, True, True) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\viewdockx\pdbqt.py"", line 6, in open_pdbqt _extract_metadata(session, f, structures) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\viewdockx\pdbqt.py"", line 34, in _extract_metadata structures[model_index].viewdockx_data = vina_values IndexError: list index out of range IndexError: list index out of range File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\viewdockx\pdbqt.py"", line 34, in _extract_metadata structures[model_index].viewdockx_data = vina_values See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 388.16 OpenGL renderer: GeForce GTX 1060/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Acer Model: Predator G3-572 OS: Microsoft Windows 10 Home Single Language (Build 18362) Memory: 17,057,812,480 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 closed normal Input/Output duplicate all ChimeraX