Opened 6 years ago

Closed 6 years ago

#2421 closed defect (nonchimerax)

'MDFF_Mgr' object has no attribute '_c_pointer'

Reported by: Tristan Croll Owned by: Tristan Croll
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc: Eric Pettersen, Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-4.20.8-200.fc29.x86_64-x86_64-with-fedora-29-Twenty_Nine
ChimeraX Version: 0.91 (2019-09-17)
Description
Looks like there has been an API change? I haven't made any changes to ISOLDE that could have caused this. MDFF_Mgr is modeled on the `Collections` molc API.

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.91 (2019-09-17)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open xaituo_scoat_refine_4.pdb

Summary of feedback from opening xaituo_scoat_refine_4.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Date 2019-09-18 Time 20:04:40 CEST +0200 (1568829880.49 s)  
  
Ignored bad PDB record found on line 2  
REMARK PHENIX refinement  
  
Ignored bad PDB record found on line 4  
REMARK ****************** INPUT FILES AND LABELS
******************************  
  
Ignored bad PDB record found on line 5  
REMARK Reflections:  
  
Ignored bad PDB record found on line 6  
REMARK file name : /home/tic20/structure_dump/kaituo/AutoSol357_denmod.mtz  
  
45 messages similar to the above omitted  
  
Chain information for xaituo_scoat_refine_4.pdb #1  
---  
Chain | Description  
A | No description available  
  

> isolde start

> set selectionWidth 4

Missing or corrupted CRYST1 card found in the PDB file. This model will be
treated as a cryo-EM model until associated with an MTZ file containing
symmetry information.  

Chain information for xaituo_scoat_refine_4.pdb  
---  
Chain | Description  
1.3/A | No description available  
  
Done loading forcefield  

> addh

Summary of feedback from adding hydrogens to xaituo_scoat_refine_4.pdb #1.3  
---  
notes | No usable SEQRES records for xaituo_scoat_refine_4.pdb (#1.3) chain A;
guessing termini instead  
Chain-initial residues that are actual N termini: /A GLU 45  
Chain-initial residues that are not actual N termini: /A GLY 118  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A PHE 676, /A ALA 116  
558 hydrogen bonds  
Adding 'H' to /A GLY 118  
/A PHE 676 is not terminus, removing H atom from 'C'  
/A ALA 116 is not terminus, removing H atom from 'C'  
4738 hydrogens added  
  
(CLIPPER) NOTE: No symmetry information found in model. Using symmetry from
MTZ file.  

> hide HC

> close #1.1.1.5

> set bgColor white

> select #1

9376 atoms, 9441 bonds, 11 pseudobonds, 27 models selected  
Bad residue number: 483  
Doing nothing  

> addh metalDist 1

Summary of feedback from adding hydrogens to xaituo_scoat_refine_4.pdb #1.3  
---  
notes | No usable SEQRES records for xaituo_scoat_refine_4.pdb (#1.3) chain A;
guessing termini instead  
Chain-initial residues that are actual N termini: /A GLU 45  
Chain-initial residues that are not actual N termini: /A GLY 118  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A PHE 676, /A ALA 116  
541 hydrogen bonds  
/A PHE 676 is not terminus, removing H atom from 'C'  
/A ALA 116 is not terminus, removing H atom from 'C'  
1 hydrogens added  
  

> select #1

9377 atoms, 9442 bonds, 11 pseudobonds, 32 models selected  

> toolshed show Shell

/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/IPython/core/history.py:226: UserWarning: IPython History requires
SQLite, your history will not be saved  
warn("IPython History requires SQLite, your history will not be saved")  

> color sel bychain

> color sel byhetero

> select clear

> select clear

Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/tic20/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 2107, in _apply_backrub  
apply_backrub(self, mdff_mgr, res)  
File "/home/tic20/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/refine/backrub_rotamer.py", line 409, in
apply_backrub  
map_weight = mdff_mgr.global_k  
File "/home/tic20/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/molobject.py", line 1800, in _get_global_k  
return f(self._c_pointer)  
AttributeError: 'MDFF_Mgr' object has no attribute '_c_pointer'  
  
Error processing trigger "sim paused":  
AttributeError: 'MDFF_Mgr' object has no attribute '_c_pointer'  
  
File "/home/tic20/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/molobject.py", line 1800, in _get_global_k  
return f(self._c_pointer)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/tic20/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 2107, in _apply_backrub  
apply_backrub(self, mdff_mgr, res)  
File "/home/tic20/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/refine/backrub_rotamer.py", line 409, in
apply_backrub  
map_weight = mdff_mgr.global_k  
File "/home/tic20/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/molobject.py", line 1800, in _get_global_k  
return f(self._c_pointer)  
AttributeError: 'MDFF_Mgr' object has no attribute '_c_pointer'  
  
Error processing trigger "sim paused":  
AttributeError: 'MDFF_Mgr' object has no attribute '_c_pointer'  
  
File "/home/tic20/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/molobject.py", line 1800, in _get_global_k  
return f(self._c_pointer)  
  
See log for complete Python traceback.  
  

> select clear

Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/tic20/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 2107, in _apply_backrub  
apply_backrub(self, mdff_mgr, res)  
File "/home/tic20/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/refine/backrub_rotamer.py", line 409, in
apply_backrub  
map_weight = mdff_mgr.global_k  
File "/home/tic20/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/molobject.py", line 1800, in _get_global_k  
return f(self._c_pointer)  
AttributeError: 'MDFF_Mgr' object has no attribute '_c_pointer'  
  
Error processing trigger "sim paused":  
AttributeError: 'MDFF_Mgr' object has no attribute '_c_pointer'  
  
File "/home/tic20/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/molobject.py", line 1800, in _get_global_k  
return f(self._c_pointer)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/home/tic20/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 2097, in _backrub_rotamer  
self._apply_backrub(None, None)  
File "/home/tic20/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 2107, in _apply_backrub  
apply_backrub(self, mdff_mgr, res)  
File "/home/tic20/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/refine/backrub_rotamer.py", line 409, in
apply_backrub  
map_weight = mdff_mgr.global_k  
File "/home/tic20/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/molobject.py", line 1800, in _get_global_k  
return f(self._c_pointer)  
AttributeError: 'MDFF_Mgr' object has no attribute '_c_pointer'  
  
AttributeError: 'MDFF_Mgr' object has no attribute '_c_pointer'  
  
File "/home/tic20/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/molobject.py", line 1800, in _get_global_k  
return f(self._c_pointer)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/tic20/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 2107, in _apply_backrub  
apply_backrub(self, mdff_mgr, res)  
File "/home/tic20/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/refine/backrub_rotamer.py", line 409, in
apply_backrub  
map_weight = mdff_mgr.global_k  
File "/home/tic20/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/molobject.py", line 1800, in _get_global_k  
return f(self._c_pointer)  
AttributeError: 'MDFF_Mgr' object has no attribute '_c_pointer'  
  
Error processing trigger "sim paused":  
AttributeError: 'MDFF_Mgr' object has no attribute '_c_pointer'  
  
File "/home/tic20/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/molobject.py", line 1800, in _get_global_k  
return f(self._c_pointer)  
  
See log for complete Python traceback.  
  

> select down

2 atoms, 1 bond, 1 model selected  

> select clear

Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/tic20/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 2107, in _apply_backrub  
apply_backrub(self, mdff_mgr, res)  
File "/home/tic20/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/refine/backrub_rotamer.py", line 409, in
apply_backrub  
map_weight = mdff_mgr.global_k  
File "/home/tic20/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/molobject.py", line 1800, in _get_global_k  
return f(self._c_pointer)  
AttributeError: 'MDFF_Mgr' object has no attribute '_c_pointer'  
  
Error processing trigger "sim paused":  
AttributeError: 'MDFF_Mgr' object has no attribute '_c_pointer'  
  
File "/home/tic20/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/molobject.py", line 1800, in _get_global_k  
return f(self._c_pointer)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/tic20/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 2107, in _apply_backrub  
apply_backrub(self, mdff_mgr, res)  
File "/home/tic20/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/refine/backrub_rotamer.py", line 409, in
apply_backrub  
map_weight = mdff_mgr.global_k  
File "/home/tic20/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/molobject.py", line 1800, in _get_global_k  
return f(self._c_pointer)  
AttributeError: 'MDFF_Mgr' object has no attribute '_c_pointer'  
  
Error processing trigger "sim paused":  
AttributeError: 'MDFF_Mgr' object has no attribute '_c_pointer'  
  
File "/home/tic20/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/molobject.py", line 1800, in _get_global_k  
return f(self._c_pointer)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/tic20/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 2107, in _apply_backrub  
apply_backrub(self, mdff_mgr, res)  
File "/home/tic20/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/refine/backrub_rotamer.py", line 409, in
apply_backrub  
map_weight = mdff_mgr.global_k  
File "/home/tic20/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/molobject.py", line 1800, in _get_global_k  
return f(self._c_pointer)  
AttributeError: 'MDFF_Mgr' object has no attribute '_c_pointer'  
  
Error processing trigger "sim paused":  
AttributeError: 'MDFF_Mgr' object has no attribute '_c_pointer'  
  
File "/home/tic20/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/molobject.py", line 1800, in _get_global_k  
return f(self._c_pointer)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 410.93
OpenGL renderer: GeForce GTX 1070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Change History (3)

comment:1 by Eric Pettersen, 6 years ago

Cc: Eric Pettersen Tom Goddard added
Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → 'MDFF_Mgr' object has no attribute '_c_pointer'

Hi Tristan,

I guess the first thing is that Collections don't have _c_pointer attributes -- they have _c_pointers attributes, and therefore your MDFF_Mgr object seems to be an individual ctypes-wrapped Python/C++ object rather than a Collection. On the C++ side, does MDFF_Mgr inherit from PythonInstance? If so, the _c_pointer attribute will be deleted in the PythonInstance destructor, which implies that your C++ MDFF_Mgr destructor got called prior to the error reported in this ticket. Perhaps putting a print statement in the MDFF_Mgr destructor might shed light on what's going on.

--Eric

in reply to:  2 ; comment:2 by Tristan Croll, 6 years ago 

Ah! Yes, sorry, not a Collection but is a PythonInstance (sorry - big day). And I think you just clued me in to what’s wrong, and if so it *is* my fault. Will check it out tomorrow - meanwhile feel free to close this.

comment:3 by Eric Pettersen, 6 years ago

Resolution: → nonchimerax
Status: assigned → closed

Okey dokey. :-)

Note: See TracTickets for help on using tickets.