Error opening PDBQT

[andrew.guy@…]

The following bug report has been submitted:
Platform:        Linux-5.3.0-64-generic-x86_64-with-debian-buster-sid
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
Error when loading PDBQT file (attached). Error not present in v0.91, but noticed in v1.0. Error present in both Windows 10 and Ubuntu install.


Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Some installed bundles are out of date.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)

  

> open /home/andrew/Downloads/new1_out.pdbqt

Summary of feedback from opening /home/andrew/Downloads/new1_out.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -7.7 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK Name = SN00783310  
  
Ignored bad PDB record found on line 4  
REMARK 4 active torsions:  
  
Ignored bad PDB record found on line 5  
REMARK status: ('A' for Active; 'I' for Inactive)  
  
Ignored bad PDB record found on line 6  
REMARK 1 A between atoms: C_1 and C_5  
  
166 messages similar to the above omitted  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 519, in dropEvent  
_open_dropped_file(self.session, p)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 1721, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 101, in cmd_open  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 152, in provider_open  
name or model_name_from_path(fi.file_name)), provider_kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 382, in collated_open  
return func(*func_args, **func_kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/viewdockx/__init__.py", line 56, in open  
return opener(session, data, file_name, True, True)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/viewdockx/pdbqt.py", line 6, in open_pdbqt  
_extract_metadata(session, f, structures)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/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 "/usr/lib/ucsf-chimerax/lib/python3.7/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 435.21
OpenGL renderer: GeForce GTX 1070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: To Be Filled By O.E.M.
Model: To Be Filled By O.E.M.
OS: Ubuntu 19.10 eoan
Architecture: 64bit ELF
CPU: 16 AMD Ryzen 7 3700X 8-Core Processor
Cache Size: 512 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           62Gi       4.8Gi        51Gi       707Mi       6.2Gi        56Gi
	Swap:         2.0Gi          0B       2.0Gi

Graphics:
	0e:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP104 [GeForce GTX 1070] [10de:1b81] (rev a1)	
	Subsystem: eVga.com. Corp. GP104 [GeForce GTX 1070] [3842:6173]	
	Kernel driver in use: nvidia
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8
File attachment: new1_1.pdbqt

new1_1.pdbqt​

[andrew.guy@…]

Added by email2trac

[Eric Pettersen]

Hi Andrew,

Thanks for reporting this problem. It is fixed in the current release, 1.1, out today, so if you get that then things should work.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab