ISOLDE simulation stopped: 'OpenMM_Thread_Handler' object has no attribute '_c_pointer'

[josep.font@…]

The following bug report has been submitted:
Platform:        Darwin-19.4.0-x86_64-i386-64bit
ChimeraX Version: 0.92 (2020-02-05)
Description
Start a simulation of a trimer of 1200 residues to fix clashes. Clashes are fixed. I tried to stop the simulation to save the changes and got this error.


Log:
UCSF ChimeraX version: 0.92 (2020-02-05)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/pep/Desktop/Pep/papers/Crosslinkingpaper/cryoEmstructuresdeposition/TrimeriOFS/trimeriOFSfinal_7_isolde.pdb

Chain information for trimeriOFSfinal_7_isolde.pdb #1  
---  
Chain | Description  
A B C | No description available  
  

> open
> /Users/pep/Desktop/Pep/papers/Crosslinkingpaper/cryoEmstructuresdeposition/TrimeriOFS/trimermapfinal.mrc

Opened trimermapfinal.mrc, grid size 256,256,256, pixel 0.986, shown at level
0.0154, step 1, values float32  

> volume #2 level 0.03506

> toolshed show ISOLDE

> set selectionWidth 4

Chain information for trimeriOFSfinal_7_isolde.pdb  
---  
Chain | Description  
1.1/A 1.1/B 1.1/C | No description available  
  
Done loading forcefield  

No template found for residue A501 (ASP)  

Adding hydrogens  
Summary of feedback from adding hydrogens to trimeriOFSfinal_7_isolde.pdb #1.1  
---  
notes | No usable SEQRES records for trimeriOFSfinal_7_isolde.pdb (#1.1) chain
A; guessing termini instead  
No usable SEQRES records for trimeriOFSfinal_7_isolde.pdb (#1.1) chain B;
guessing termini instead  
No usable SEQRES records for trimeriOFSfinal_7_isolde.pdb (#1.1) chain C;
guessing termini instead  
Chain-initial residues that are actual N termini: /A LYS 6, /B LYS 6, /C LYS 6  
Chain-initial residues that are not actual N termini: /A PRO 129, /B PRO 129,
/C PRO 129  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A GLU 416, /A HIS 114, /B
GLU 416, /B HIS 114, /C GLU 416, /C HIS 114  
982 hydrogen bonds  
/A GLU 416 is not terminus, removing H atom from 'C'  
/A HIS 114 is not terminus, removing H atom from 'C'  
/B GLU 416 is not terminus, removing H atom from 'C'  
/B HIS 114 is not terminus, removing H atom from 'C'  
/C GLU 416 is not terminus, removing H atom from 'C'  
1 messages similar to the above omitted  
0 hydrogens added  
  

No template found for residue A501 (ASP)  

Excluding residue  

No template found for residue B501 (ASP)  

Excluding residue  

No template found for residue C501 (ASP)  

Excluding residue  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/Users/pep/Library/Application Support/ChimeraX/0.92/site-
packages/chimerax/isolde/delayed_reaction.py", line 64, in callback  
if self.tf is None or self.tf():  
File "/Users/pep/Library/Application Support/ChimeraX/0.92/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 241, in
thread_finished  
return f(self._c_pointer)  
AttributeError: 'OpenMM_Thread_Handler' object has no attribute '_c_pointer'  
  
Error processing trigger "new frame":  
AttributeError: 'OpenMM_Thread_Handler' object has no attribute '_c_pointer'  
  
File "/Users/pep/Library/Application Support/ChimeraX/0.92/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 241, in
thread_finished  
return f(self._c_pointer)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-14.5.22
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.

[Tristan Croll]

Hmm... that's an interesting one. Should be easy enough to prevent the traceback, but I'm really surprised that it could happen at all. Will look into how it came about. Meanwhile, I'm curious what's wrong with those unrecognised ASP residues - there's not many ways that can happen. Truncations to ala/gly are supported (the carbon at the truncation point should be bare)... if the backbone nitrogen is too near a metal, AddH won't protonate it - try addh metaldist 1 if that's your situation. The other possibility I can think of: most free single amino acids aren't current supported (something I'm working on fixing).

[josep.font@…]

Thanks a lot

JOSEP (Pep) FONT SADURNI  | PhD
Lecturer 
Academic Leader Research Education (Postgraduate Coordinator)
School of Medical Sciences 
Faculty of Medicine and Health

THE UNIVERSITY OF SYDNEY
Rm 508, Molecular Bioscience Building, G08 | The University of Sydney | NSW | 2006
T +61 2 9114 1458 <tel:+61%202%209114%201458> | M +61 04 3204 3331 <tel:+61%2004%203204%203331>
E josep.font@sydney.edu.au| W http://sydney.edu.au <http://sydney.edu.au/>
 

On 18/4/20, 2:34 am, "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:

    #3065: ISOLDE simulation stopped: 'OpenMM_Thread_Handler' object has no attribute
    '_c_pointer'
    -----------------------------------+---------------------------
              Reporter:  josep.font@…  |      Owner:  Tristan Croll
                  Type:  defect        |     Status:  assigned
              Priority:  normal        |  Milestone:
             Component:  Third Party   |    Version:
            Resolution:                |   Keywords:
            Blocked By:                |   Blocking:
    Notify when closed:                |   Platform:  all
               Project:  ChimeraX      |
    -----------------------------------+---------------------------

    Comment (by Tristan Croll):

     Hmm... that's an interesting one. Should be easy enough to prevent the
     traceback, but I'm really surprised that it could happen at all. Will look
     into how it came about. Meanwhile, I'm curious what's wrong with those
     unrecognised ASP residues - there's not many ways that can happen.
     Truncations to ala/gly are supported (the carbon at the truncation point
     should be bare)... if the backbone nitrogen is too near a metal, `AddH`
     won't protonate it - try `addh metaldist 1` if that's your situation. The
     other possibility I can think of: most free single amino acids aren't
     current supported (something I'm working on fixing).

    --
    Ticket URL: <https://protect-au.mimecast.com/s/X_yLCQnMBZf9RooQIx5b9V?domain=plato.cgl.ucsf.edu>
    ChimeraX <https://protect-au.mimecast.com/s/cUfPCROND2uQO556FNP0pG?domain=rbvi.ucsf.edu>
    ChimeraX Issue Tracker

[Tristan Croll]

Finally tracked down and squished. Will be fixed in the next release.