Opened 5 years ago

Closed 5 years ago

#3495 closed defect (fixed)

ViewDockX no longer handling .pdbqt file

Reported by: tongc@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

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
Attempted to open a Vina output file containing a ligand as well as the flexible residues surrounding it (the protein's rigid structure was not in the file). This also occured with files that did not contain the flexible residues, only ligand conformations

Log:
Startup Messages  
---  
note | Some installed bundles are out of date. Please update the following
bundles:

  * UI to version 1.2.1 (currently 1.0)
  * UI to version 1.2 (currently 1.0)

  
  
  
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
> C:/Users/caitl/Desktop/Fellowship/Trials/4hydroxytamoxifen/4hydroxytamoxifen_outF1.pdbqt

Summary of feedback from opening
C:/Users/caitl/Desktop/Fellowship/Trials/4hydroxytamoxifen/4hydroxytamoxifen_outF1.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -5.9 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: C_1 and C_7  
  
Ignored bad PDB record found on line 6  
REMARK 2 A between atoms: C_4 and O_23  
  
310 messages similar to the above omitted  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py",
line 519, in dropEvent  
_open_dropped_file(self.session, p)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py",
line 1721, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(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 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/caitl/Desktop/Fellowship/Trials/4hydroxytamoxifen/4hydroxytamoxifen_outF1.pdbqt

Summary of feedback from opening
C:/Users/caitl/Desktop/Fellowship/Trials/4hydroxytamoxifen/4hydroxytamoxifen_outF1.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -5.9 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: C_1 and C_7  
  
Ignored bad PDB record found on line 6  
REMARK 2 A between atoms: C_4 and O_23  
  
310 messages similar to the above omitted  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py",
line 519, in dropEvent  
_open_dropped_file(self.session, p)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py",
line 1721, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(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 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/caitl/Desktop/Fellowship/Trials/4hydroxytamoxifen/Output/4hydroxytamoxifen_out3.pdbqt

Summary of feedback from opening
C:/Users/caitl/Desktop/Fellowship/Trials/4hydroxytamoxifen/Output/4hydroxytamoxifen_out3.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -9.3 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: C_1 and C_7  
  
Ignored bad PDB record found on line 6  
REMARK 2 A between atoms: C_4 and O_23  
  
61 messages similar to the above omitted  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py",
line 519, in dropEvent  
_open_dropped_file(self.session, p)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py",
line 1721, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(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 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/caitl/Desktop/Fellowship/Trials/4hydroxytamoxifen/Output/4hydroxytamoxifen_out1.pdbqt

Summary of feedback from opening
C:/Users/caitl/Desktop/Fellowship/Trials/4hydroxytamoxifen/Output/4hydroxytamoxifen_out1.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -9.4 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: C_1 and C_7  
  
Ignored bad PDB record found on line 6  
REMARK 2 A between atoms: C_4 and O_23  
  
61 messages similar to the above omitted  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 150, in _qt_safe  
if data_format is None else " format " +
StringArg.unparse(data_format.nicknames[0])))  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(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 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/caitl/Desktop/Fellowship/Trials/4hydroxytamoxifen/3ert_ERalpha_flex.pdbqt

Summary of feedback from opening
C:/Users/caitl/Desktop/Fellowship/Trials/4hydroxytamoxifen/3ert_ERalpha_flex.pdbqt  
---  
warnings | Ignored bad PDB record found on line 1  
BEGIN_RES HIS A 524  
  
Ignored bad PDB record found on line 2  
REMARK 2 active torsions:  
  
Ignored bad PDB record found on line 3  
REMARK status: ('A' for Active; 'I' for Inactive)  
  
Ignored bad PDB record found on line 4  
REMARK 1 A between atoms: CA and CB  
  
Ignored bad PDB record found on line 5  
REMARK 2 A between atoms: CB and CG  
  
67 messages similar to the above omitted  
  
Chain information for 3ert_ERalpha_flex.pdbqt #1  
---  
Chain | Description  
A | No description available  
  
Opened 3ert_ERalpha_flex.pdbqt containing 1 structures (31 atoms, 27 bonds)  

> open
> C:/Users/caitl/Desktop/Fellowship/Trials/4hydroxytamoxifen/4hydroxytamoxifen_outF1.pdbqt

Summary of feedback from opening
C:/Users/caitl/Desktop/Fellowship/Trials/4hydroxytamoxifen/4hydroxytamoxifen_outF1.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -5.9 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: C_1 and C_7  
  
Ignored bad PDB record found on line 6  
REMARK 2 A between atoms: C_4 and O_23  
  
310 messages similar to the above omitted  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\ui\graphics.py", line 51, in event  
if self.handle_drag_and_drop(event):  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\ui\graphics.py", line 116, in handle_drag_and_drop  
mw.dropEvent(event)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py",
line 519, in dropEvent  
_open_dropped_file(self.session, p)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py",
line 1721, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(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 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.  
  

> close session

> open
> C:/Users/caitl/Desktop/Fellowship/Trials/4hydroxytamoxifen/3ert_ERalpha_rigid.pdbqt

Chain information for 3ert_ERalpha_rigid.pdbqt #1  
---  
Chain | Description  
A | No description available  
  
Opened 3ert_ERalpha_rigid.pdbqt containing 1 structures (1962 atoms, 2024
bonds)  

> ui tool show ViewDockX

No suitable models found for ViewDockX  

> toolshed show

> ui tool show ViewDockX

No suitable models found for ViewDockX  

> open
> C:/Users/caitl/Desktop/Fellowship/Trials/4hydroxytamoxifen/3ert_ERalpha_flex.pdbqt

Summary of feedback from opening
C:/Users/caitl/Desktop/Fellowship/Trials/4hydroxytamoxifen/3ert_ERalpha_flex.pdbqt  
---  
warnings | Ignored bad PDB record found on line 1  
BEGIN_RES HIS A 524  
  
Ignored bad PDB record found on line 2  
REMARK 2 active torsions:  
  
Ignored bad PDB record found on line 3  
REMARK status: ('A' for Active; 'I' for Inactive)  
  
Ignored bad PDB record found on line 4  
REMARK 1 A between atoms: CA and CB  
  
Ignored bad PDB record found on line 5  
REMARK 2 A between atoms: CB and CG  
  
67 messages similar to the above omitted  
  
Chain information for 3ert_ERalpha_flex.pdbqt #2  
---  
Chain | Description  
A | No description available  
  
Opened 3ert_ERalpha_flex.pdbqt containing 1 structures (31 atoms, 27 bonds)  

> open
> C:/Users/caitl/Desktop/Fellowship/Trials/4hydroxytamoxifen/4hydroxytamoxifen.pdbqt

Summary of feedback from opening
C:/Users/caitl/Desktop/Fellowship/Trials/4hydroxytamoxifen/4hydroxytamoxifen.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: C_1 and C_7  
  
Ignored bad PDB record found on line 4  
REMARK 2 A between atoms: C_4 and O_23  
  
Ignored bad PDB record found on line 5  
REMARK 3 A between atoms: C_7 and C_8  
  
27 messages similar to the above omitted  
  
Opened 4hydroxytamoxifen.pdbqt containing 1 structures (30 atoms, 32 bonds)  

> open
> C:/Users/caitl/Desktop/Fellowship/Trials/4hydroxytamoxifen/4hydroxytamoxifen_outF1.pdbqt

Summary of feedback from opening
C:/Users/caitl/Desktop/Fellowship/Trials/4hydroxytamoxifen/4hydroxytamoxifen_outF1.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -5.9 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: C_1 and C_7  
  
Ignored bad PDB record found on line 6  
REMARK 2 A between atoms: C_4 and O_23  
  
310 messages similar to the above omitted  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\ui\graphics.py", line 51, in event  
if self.handle_drag_and_drop(event):  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\ui\graphics.py", line 116, in handle_drag_and_drop  
mw.dropEvent(event)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py",
line 519, in dropEvent  
_open_dropped_file(self.session, p)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py",
line 1721, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(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 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.  
  

> close session

> open
> C:/Users/caitl/Desktop/Fellowship/Trials/4hydroxytamoxifen/4hydroxytamoxifen_outF1.pdbqt

Summary of feedback from opening
C:/Users/caitl/Desktop/Fellowship/Trials/4hydroxytamoxifen/4hydroxytamoxifen_outF1.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -5.9 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: C_1 and C_7  
  
Ignored bad PDB record found on line 6  
REMARK 2 A between atoms: C_4 and O_23  
  
310 messages similar to the above omitted  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py",
line 519, in dropEvent  
_open_dropped_file(self.session, p)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py",
line 1721, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(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 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 451.67
OpenGL renderer: GeForce GTX 960M/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: XPS 15 9550
OS: Microsoft Windows 10 Pro (Build 18362)
Memory: 17,034,719,232
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-6700HQ CPU @ 2.60GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8
File attachment: 4hydroxytamoxifen_outF1.pdbqt

4hydroxytamoxifen_outF1.pdbqt​

Attachments (1)

4hydroxytamoxifen_outF1.pdbqt​ (22.7 KB ) - added by tongc@… 5 years ago.
Added by email2trac

Download all attachments as: .zip

Change History (3)

by tongc@…, 5 years ago

Attachment: 4hydroxytamoxifen_outF1.pdbqt​ added

Added by email2trac

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → Input/Output
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → ViewDockX no longer handling .pdbqt file

comment:2 by Eric Pettersen, 5 years ago

Resolution: → fixed
Status: accepted → closed

Hi Caitlyn,

Thanks for reporting this problem. I have just fixed it, so if you get tomorrow's daily build you should be able to open your file. Sorry for the hassle.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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