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#3466 closed defect (fixed)

'OpenMM_Thread_Handler' object has no attribute '_c_pointer'

Reported by:	eferri@…	Owned by:	Tristan Croll
Priority:	normal	Milestone:
Component:	Third Party	Version:
Keywords:		Cc:	pett
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description (last modified by pett)

The following bug report has been submitted:
Platform:        Darwin-19.5.0-x86_64-i386-64bit
ChimeraX Version: 0.93 (2020-04-03)
Description
I am attempting to use ISOLDE on a large (8000 atoms) model and crystallographic data using a MacBook Pro. The interface says "simulation is running" but nothing moves. I tried to stop the simulation. I get this error.

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.93 (2020-04-03)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed show ISOLDE

> set selectionWidth 4

Done loading forcefield  

> open2 "almost_final.pdb"

Summary of feedback from opening <_io.textiowrapper
name="almost_final.pdb" mode="rt"
encoding="utf-8">  
---  
warning | Ignored bad PDB record found on line 206  
LINKR ND2 ASN R 343 C1 NAG R 601 NAG-ASN  
  
almost_final.pdb title:  
\--- [more info...]  
  
Chain information for almost_final.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
H | No description available  
L | No description available  
R | No description available  
  
Non-standard residues in almost_final.pdb #1  
---  
NAG — (NAG)  
  
almost_final.pdb title:  
\--- [more info...]  
  
Chain information for almost_final.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/H | No description available  
1.2/L | No description available  
1.2/R | No description available  
  
Non-standard residues in almost_final.pdb #1.2  
---  
NAG — (NAG)  
  
Discarding unrecognised/unsupported data array /XDScrystal/XDSdataset/ISYM Y  
Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  

> volume #!1.1.1.2-4 style surface

> transparency #1.1.1.2.1#1.1.1.3.1-2#1.1.1.4.1 0

> transparency #1.1.1.2.1#1.1.1.3.1-2#1.1.1.4.1 50

> volume #!1.1.1.2-4 showOutlineBox true

> volume #!1.1.1.2-4 showOutlineBox false

> addh

Summary of feedback from adding hydrogens to almost_final.pdb #1.2  
---  
notes | No usable SEQRES records for almost_final.pdb (#1.2) chain A; guessing
termini instead  
No usable SEQRES records for almost_final.pdb (#1.2) chain B; guessing termini
instead  
No usable SEQRES records for almost_final.pdb (#1.2) chain H; guessing termini
instead  
No usable SEQRES records for almost_final.pdb (#1.2) chain L; guessing termini
instead  
No usable SEQRES records for almost_final.pdb (#1.2) chain R; guessing termini
instead  
Chain-initial residues that are actual N termini: /A GLN 1, /B GLU 1, /H VAL
2, /L ASP 1, /R PRO 330  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A SER 229, /B GLU 213, /H LYS
221, /L GLU 214, /R LYS 528  
Chain-final residues that are not actual C termini:  
980 hydrogen bonds  
7962 hydrogens added  
  

> hide HC

> select #1.2

16185 atoms, 16396 bonds, 5 models selected  

No template found for residue R601 (NAG)  

Excluding residue  
Updating bulk solvent parameters...  
Updating bulk solvent parameters...  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.93.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/elenaferri/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/delayed_reaction.py", line 64, in callback  
if self.tf is None or self.tf():  
File "/Users/elenaferri/Library/Application Support/ChimeraX/0.93/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/elenaferri/Library/Application Support/ChimeraX/0.93/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 ATI-3.9.15
OpenGL renderer: AMD Radeon Pro Vega 16 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Change History (5)

in reply to: 1 ; follow-up: 1 comment:1 by eferri@…, 5 years ago

Please disregard this email. Confidential model information is included and I did not know that would happen.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Wednesday, July 1, 2020 12:51:59 PM
To: Elena Ferri <eferri@vir.bio>
Subject: [EXTERNAL] [ChimeraX] #3466: ChimeraX bug report submission

** EXTERNAL EMAIL **

#3466: ChimeraX bug report submission
------------------------+-----------------------------
 Reporter:  eferri@…    |                Type:  defect
   Status:  new         |            Priority:  normal
Component:  Unassigned  |          Blocked By:
 Blocking:              |  Notify when closed:
------------------------+-----------------------------
 {{{
 The following bug report has been submitted:
 Platform:        Darwin-19.5.0-x86_64-i386-64bit
 ChimeraX Version: 0.93 (2020-04-03)
 Description
 I am attempting to use ISOLDE on a large (8000 atoms) model and
 crystallographic data using a MacBook Pro. The interface says "simulation
 is running" but nothing moves. I tried to stop the simulation. I get this
 error.

 Log:
 Startup Messages
 ---
 warning | 'clip' is a prefix of an existing command 'clipper'

 UCSF ChimeraX version: 0.93 (2020-04-03)
 © 2016-2020 Regents of the University of California. All rights reserved.
 How to cite UCSF ChimeraX

 > toolshed show ISOLDE

 > set selectionWidth 4

 Done loading forcefield

 > open2 "almost_final.pdb"

 Summary of feedback from opening <_io.textiowrapper
 name="almost_final.pdb" mode="rt"
 encoding="utf-8">
 ---
 warning | Ignored bad PDB record found on line 206
 LINKR ND2 ASN R 343 C1 NAG R 601 NAG-ASN

 almost_final.pdb title:
 \--- [more info...]

 Chain information for almost_final.pdb #1
 ---
 Chain | Description
 A | No description available
 B | No description available
 H | No description available
 L | No description available
 R | No description available

 Non-standard residues in almost_final.pdb #1
 ---
 NAG — (NAG)

 almost_final.pdb title:
 \--- [more info...]

 Chain information for almost_final.pdb
 ---
 Chain | Description
 1.2/A | No description available
 1.2/B | No description available
 1.2/H | No description available
 1.2/L | No description available
 1.2/R | No description available

 Non-standard residues in almost_final.pdb #1.2
 ---
 NAG — (NAG)

 Discarding unrecognised/unsupported data array /XDScrystal/XDSdataset/ISYM
 Y
 Reflection data provided as intensities. Performing French & Wilson
 scaling to
 convert to amplitudes...

 > volume #!1.1.1.2-4 style surface

 > transparency #1.1.1.2.1#1.1.1.3.1-2#1.1.1.4.1 0

 > transparency #1.1.1.2.1#1.1.1.3.1-2#1.1.1.4.1 50

 > volume #!1.1.1.2-4 showOutlineBox true

 > volume #!1.1.1.2-4 showOutlineBox false

 > addh

 Summary of feedback from adding hydrogens to almost_final.pdb #1.2
 ---
 notes | No usable SEQRES records for almost_final.pdb (#1.2) chain A;
 guessing
 termini instead
 No usable SEQRES records for almost_final.pdb (#1.2) chain B; guessing
 termini
 instead
 No usable SEQRES records for almost_final.pdb (#1.2) chain H; guessing
 termini
 instead
 No usable SEQRES records for almost_final.pdb (#1.2) chain L; guessing
 termini
 instead
 No usable SEQRES records for almost_final.pdb (#1.2) chain R; guessing
 termini
 instead
 Chain-initial residues that are actual N termini: /A GLN 1, /B GLU 1, /H
 VAL
 2, /L ASP 1, /R PRO 330
 Chain-initial residues that are not actual N termini:
 Chain-final residues that are actual C termini: /A SER 229, /B GLU 213, /H
 LYS
 221, /L GLU 214, /R LYS 528
 Chain-final residues that are not actual C termini:
 980 hydrogen bonds
 7962 hydrogens added

 > hide HC

 > select #1.2

 16185 atoms, 16396 bonds, 5 models selected

 No template found for residue R601 (NAG)

 Excluding residue
 Updating bulk solvent parameters...
 Updating bulk solvent parameters...
 Traceback (most recent call last):
 File
 "/Applications/ChimeraX-0.93.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/elenaferri/Library/Application Support/ChimeraX/0.93/site-
 packages/chimerax/isolde/delayed_reaction.py", line 64, in callback
 if https://urldefense.proofpoint.com/v2/url?u=http-3A__self.tf&d=DwIGaQ&c=euGZstcaTDllvimEN8b7jXrwqOf-v5A_CdpgnVfiiMM&r=fZOHi-tiPMYVE6S8GFw7Mg&m=PZx5iVA-kSBMTJs_hgafQ44pH987vpFUbiav2XCiQg8&s=iwEYixE0U8Gq2zFnb67RdX9MI_4DsXU0RXe-blsGP4I&e= is None or self.tf():
 File "/Users/elenaferri/Library/Application Support/ChimeraX/0.93/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/elenaferri/Library/Application Support/ChimeraX/0.93/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 ATI-3.9.15
 OpenGL renderer: AMD Radeon Pro Vega 16 OpenGL Engine
 OpenGL vendor: ATI Technologies Inc.

 }}}

--
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ChimeraX <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimerax_&d=DwIGaQ&c=euGZstcaTDllvimEN8b7jXrwqOf-v5A_CdpgnVfiiMM&r=fZOHi-tiPMYVE6S8GFw7Mg&m=PZx5iVA-kSBMTJs_hgafQ44pH987vpFUbiav2XCiQg8&s=YYGdd6g_r2yOfJyC1cEiOzliXRIDDIneD7N6KErAsI4&e=>
ChimeraX Issue Tracker

Last edited 5 years ago by pett (previous) (diff)

comment:2 by pett, 5 years ago

Component:	Unassigned → Third Party
Description:	modified (diff)
Owner:	set to Tristan Croll
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → 'OpenMM_Thread_Handler' object has no attribute '_c_pointer'

comment:3 by pett, 5 years ago

Cc:	pett added

Hi Elena,

I have edited the ticket to remove data-specific information (namely the folder containing "almost_final.pdb"). If there are other things I should remove, please let me know. If you still want the entire ticket deleted, I can do that too.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

in reply to: 4 ; follow-up: 4 comment:4 by eferri@…, 5 years ago

Thanks Eric,

Much appreciated. The ticket can proceed with these edits. Thanks!

Elena

--
Elena Ferri, PhD
Scientist, Protein Chemistry and Structural Biology
(she/her/hers)
 
VIR Biotechnology, Inc.
499 Illinois Street, 5th floor
San Francisco, CA 94158
--
CONFIDENTIAL
Information contained herein is considered Confidential because it is not generally known to the public and disclosure of this information could harm our business.
 

On 7/2/20, 9:19 AM, "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:

    ** EXTERNAL EMAIL **


    #3466: 'OpenMM_Thread_Handler' object has no attribute '_c_pointer'
    ----------------------------------+---------------------------
              Reporter:  eferri@…     |      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     |
    ----------------------------------+---------------------------
    Changes (by Eric Pettersen):

     * cc: Eric Pettersen (added)


    Comment:

     Hi Elena,
             I have edited the ticket to remove data-specific information
     (namely the folder containing "almost_final.pdb").  If there are other
     things I should remove, please let me know.  If you still want the entire
     ticket deleted, I can do that too.

     --Eric

             Eric Pettersen
             UCSF Computer Graphics Lab

    --
    Ticket URL: <https://urldefense.proofpoint.com/v2/url?u=https-3A__plato.cgl.ucsf.edu_trac_ChimeraX_ticket_3466-23comment-3A3&d=DwIGaQ&c=euGZstcaTDllvimEN8b7jXrwqOf-v5A_CdpgnVfiiMM&r=fZOHi-tiPMYVE6S8GFw7Mg&m=B8N0GcvaxGsEAlgA9yRBzY6OdrbH-_ykNQtqm6xHAK4&s=zF3Pm0afIxyZxJVMnUptZcByUamXc1-WFRycN7_o2dk&e=>
    ChimeraX <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimerax_&d=DwIGaQ&c=euGZstcaTDllvimEN8b7jXrwqOf-v5A_CdpgnVfiiMM&r=fZOHi-tiPMYVE6S8GFw7Mg&m=B8N0GcvaxGsEAlgA9yRBzY6OdrbH-_ykNQtqm6xHAK4&s=4ZpGeQaL5IBxxB9GPxwcNEzTkatUOTJw70cxuo-7pIo&e=>
    ChimeraX Issue Tracker

comment:5 by Tristan Croll, 4 years ago

Resolution:	→ fixed
Status:	assigned → closed

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

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