open .pdbqt: list index out of range

[santiago.jus.are@…]

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

[Eric Pettersen]

Hi Santiago,

Thanks for reporting this problem. It was fixed a few days ago, so if you get the current ChimeraX daily build, so you should be able to open your file without problem. Sorry for the inconvenience.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab