Opened 4 years ago

Closed 4 years ago

Last modified 4 years ago

#5363 closed defect (not a bug)

MolecularDynamicsViewer format

Reported by: finnegan.73@… Owned by: pett
Priority: normal Milestone:
Component: MD/Ensemble Analysis Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
I thought I might be able to generate a PDB file for my simulation trajectory using VMD and then load it into this program for visualizatoin. It seems it has some python error in the gui.py file when I try to read my PDB file. Is there any specific format this needs to be in? At present I have molecules seperated by TERs and frames separated by ENDs. Thanks in advance for any help you can give!

Also, here is the error that it outputs when I try to load in my pdb:

IndexError: list index out of range

File "C:\My\path\to\chimeral\UCSF\ChimeraX\1.2\site-packages\com\kdiller\dynamics\viewer\gui.py", line 227, in openFile
self.atomStruct.atoms.coords = self.atomLocation[0]

See log for complete Python traceback.

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed show

Downloading bundle MolecularDynamicsViewer-1.2-py3-none-any.whl  
Successfully installed MolecularDynamicsViewer-1.2  
Installed MolecularDynamicsViewer (1.2)  

> ui tool show "Molecular Dynamics Viewer"

Please register the custom scheme 'kmd' via
QWebEngineUrlScheme::registerScheme() before installing the custom scheme
handler.  

> amber 0 7500

Unknown command: amber 0 7500  

> MD MOvie

Unknown command: MD MOvie  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 324, in interceptRequest  
self._callback(info)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 85, in _intercept  
return interceptor(request_info, *args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\htmltool.py", line 112, in _navigate  
self.session.ui.thread_safe(self.handle_scheme, url)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 366, in thread_safe  
func(*args, **kw)  
File "C:\Users\tjffi\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\com\kdiller\dynamics\viewer\gui.py", line 57, in handle_scheme  
self.openFile()  
File "C:\Users\tjffi\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\com\kdiller\dynamics\viewer\gui.py", line 227, in openFile  
self.atomStruct.atoms.coords = self.atomLocation[0]  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File "C:\Users\tjffi\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\com\kdiller\dynamics\viewer\gui.py", line 227, in openFile  
self.atomStruct.atoms.coords = self.atomLocation[0]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 324, in interceptRequest  
self._callback(info)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 85, in _intercept  
return interceptor(request_info, *args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\htmltool.py", line 112, in _navigate  
self.session.ui.thread_safe(self.handle_scheme, url)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 366, in thread_safe  
func(*args, **kw)  
File "C:\Users\tjffi\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\com\kdiller\dynamics\viewer\gui.py", line 57, in handle_scheme  
self.openFile()  
File "C:\Users\tjffi\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\com\kdiller\dynamics\viewer\gui.py", line 227, in openFile  
self.atomStruct.atoms.coords = self.atomLocation[0]  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File "C:\Users\tjffi\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\com\kdiller\dynamics\viewer\gui.py", line 227, in openFile  
self.atomStruct.atoms.coords = self.atomLocation[0]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 324, in interceptRequest  
self._callback(info)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 85, in _intercept  
return interceptor(request_info, *args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\htmltool.py", line 112, in _navigate  
self.session.ui.thread_safe(self.handle_scheme, url)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 366, in thread_safe  
func(*args, **kw)  
File "C:\Users\tjffi\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\com\kdiller\dynamics\viewer\gui.py", line 57, in handle_scheme  
self.openFile()  
File "C:\Users\tjffi\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\com\kdiller\dynamics\viewer\gui.py", line 227, in openFile  
self.atomStruct.atoms.coords = self.atomLocation[0]  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File "C:\Users\tjffi\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\com\kdiller\dynamics\viewer\gui.py", line 227, in openFile  
self.atomStruct.atoms.coords = self.atomLocation[0]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 324, in interceptRequest  
self._callback(info)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 85, in _intercept  
return interceptor(request_info, *args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\htmltool.py", line 112, in _navigate  
self.session.ui.thread_safe(self.handle_scheme, url)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 366, in thread_safe  
func(*args, **kw)  
File "C:\Users\tjffi\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\com\kdiller\dynamics\viewer\gui.py", line 57, in handle_scheme  
self.openFile()  
File "C:\Users\tjffi\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\com\kdiller\dynamics\viewer\gui.py", line 227, in openFile  
self.atomStruct.atoms.coords = self.atomLocation[0]  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File "C:\Users\tjffi\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\com\kdiller\dynamics\viewer\gui.py", line 227, in openFile  
self.atomStruct.atoms.coords = self.atomLocation[0]  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 461.40
OpenGL renderer: GeForce GTX 1070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: HP
Model: OMEN by HP Laptop
OS: Microsoft Windows 10 Pro (Build 19042)
Memory: 34,233,053,184
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-8750H CPU @ 2.20GHz
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
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File attachment: CAR_traj_testing.pdb

CAR_traj_testing.pdb​

Attachments (1)

CAR_traj_testing.pdb​ (89.3 MB ) - added by finnegan.73@… 4 years ago.
Added by email2trac

Change History (5)

by finnegan.73@…, 4 years ago

Attachment: CAR_traj_testing.pdb​ added

Added by email2trac

comment:1 by pett, 4 years ago

Component: Unassigned → MD/Ensemble Analysis
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → MolecularDynamicsViewer format

comment:2 by pett, 4 years ago

Resolution: → not a bug
Status: accepted → closed

Hi Tyler,

I believe the MolecularDynamicsViewer plugin expects the PDB file to be formatted the same way that NMR ensembles are formatted, i.e. each frame preceded with a MODEL record (​http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#MODEL) and followed with an ENDMDL record (​http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ENDMDL). Let me know if you need any further guidance.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

in reply to:  4 comment:3 by finnegan.73@…, 4 years ago 

Hey Eric,

Thanks for your help! Its now running smoothly with the proper delimiter.

Best,
Tyler
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Thursday, October 7, 2021 7:54 PM
Cc: Finnegan, Tyler J. <finnegan.73@buckeyemail.osu.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #5363: MolecularDynamicsViewer format

#5363: MolecularDynamicsViewer format
-------------------------------------------+----------------------------
          Reporter:  finnegan.73@…         |      Owner:  Eric Pettersen
              Type:  defect                |     Status:  closed
          Priority:  normal                |  Milestone:
         Component:  MD/Ensemble Analysis  |    Version:
        Resolution:  not a bug             |   Keywords:
        Blocked By:                        |   Blocking:
Notify when closed:                        |   Platform:  all
           Project:  ChimeraX              |
-------------------------------------------+----------------------------
Changes (by Eric Pettersen):

 * status:  accepted => closed
 * resolution:   => not a bug


Comment:

 Hi Tyler,
         I believe the MolecularDynamicsViewer plugin expects the PDB file
 to be formatted the same way that NMR ensembles are formatted, i.e. each
 frame preceded with a MODEL record (https://urldefense.com/v3/__http://www.wwpdb.org/documentation__;!!KGKeukY!nFfCum4ZknfQb6Z6nzw4gszWlpbVi4NgcEVcrmwmhgE9VzpIgUDBb7vCpJh77nHr3hb7w5dtLJzE_A$
 /file-format-content/format33/sect9.html#MODEL) and followed with an
 ENDMDL record (https://urldefense.com/v3/__http://www.wwpdb.org/documentation/file-format-__;!!KGKeukY!nFfCum4ZknfQb6Z6nzw4gszWlpbVi4NgcEVcrmwmhgE9VzpIgUDBb7vCpJh77nHr3hb7w5eHSq_0Fw$
 content/format33/sect9.html#ENDMDL).  Let me know if you need any further
 guidance.

 --Eric

         Eric Pettersen
         UCSF Computer Graphics Lab

--
Ticket URL: <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5363*comment:2__;Iw!!KGKeukY!nFfCum4ZknfQb6Z6nzw4gszWlpbVi4NgcEVcrmwmhgE9VzpIgUDBb7vCpJh77nHr3hb7w5fpNMX8hA$ >
ChimeraX <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/__;!!KGKeukY!nFfCum4ZknfQb6Z6nzw4gszWlpbVi4NgcEVcrmwmhgE9VzpIgUDBb7vCpJh77nHr3hb7w5cgMIeRZg$ >
ChimeraX Issue Tracker

comment:4 by pett, 4 years ago

Glad it's working!

--Eric

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