Structure.delete_alt_locs() failing

[Tristan Croll]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.3rc202110222254 (2021-10-22 22:54:52 UTC)
Description
Structure.delete_alt_locs() is failing. Doesn't appear to be specific to this model - also happens for 5yd4.

Log:
UCSF ChimeraX version: 1.3rc202110222254 (2021-10-22)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 7amc structureFactors true

Summary of feedback from opening 7amc fetched from pdb  
---  
warning | WARNING: multiple experimental reflection datasets found:  
F_meas_au, F_meas_sigma_au,  
pdbx_F_plus, pdbx_F_plus_sigma, pdbx_F_minus, pdbx_F_minus_sigma,  
pdbx_anom_difference, pdbx_anom_difference_sigma,  
intensity_meas, intensity_sigma,  
pdbx_I_plus, pdbx_I_plus_sigma, pdbx_I_minus, pdbx_I_minus_sigma  
Automatically choosing "F_meas_au, F_meas_sigma_au".  
notes | Fetching compressed mmCIF 7amc from
http://files.rcsb.org/download/7amc.cif  
Fetching CCD 73B from http://ligand-expo.rcsb.org/reports/7/73B/73B.cif  
Fetching CCD GOL from http://ligand-expo.rcsb.org/reports/G/GOL/GOL.cif  
Fetching compressed 7amc structure factors from
http://files.rcsb.org/download/7amc-sf.cif  
Resolution: 1.2198005988021892  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 62,66,62, pixel
0.405,0.385,0.391, shown at level 1.06, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 62,66,62, pixel
0.405,0.385,0.391, shown at level -0.172,0.172, step 1, values float32  
Opened (LIVE) 2mFo-DFc_smooth_26 as #1.1.1.4, grid size 62,66,62, pixel
0.405,0.385,0.391, shown at level 0.587, step 1, values float32  
7amc title:  
SmBRD3(2), Bromodomain 2 of the Bromodomain 3 protein from Schistosoma mansoni
in complex with iBET726 [more info...]  
  
Chain information for 7amc  
---  
Chain | Description | UniProt  
1.2/A 1.2/B | Putative bromodomain-containing protein 3, brd3 |
A0A5K4EQL3_SCHMA  
  
Non-standard residues in 7amc #1.2  
---  
73B —
4-[(2S,4R)-1-acetyl-4-[(4-chlorophenyl)amino]-2-methyl-1,2,3,4-tetrahydroquinolin-6-yl]benzoic
acid  
EDO — 1,2-ethanediol (ethylene glycol)  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
  
7amc mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> view /A:73B

> set bgColor #ffffff00

> close #1

Deleting Crystallographic maps (7amc-sf.cif)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_smooth_26  

> open 3mvs structureFactors true

Summary of feedback from opening 3mvs fetched from pdb  
---  
warning | WARNING: multiple experimental reflection datasets found:  
F_meas_au, F_meas_sigma_au,  
phase_calc, fom  
Automatically choosing "F_meas_au, F_meas_sigma_au".  
notes | Fetching compressed mmCIF 3mvs from
http://files.rcsb.org/download/3mvs.cif  
Fetching CCD CA from http://ligand-expo.rcsb.org/reports/C/CA/CA.cif  
Fetching compressed 3mvs structure factors from
http://files.rcsb.org/download/3mvs-sf.cif  
Resolution: 1.0964302375059438  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 96,70,72, pixel
0.355,0.357,0.363, shown at level 1.4, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 96,70,72, pixel
0.355,0.357,0.363, shown at level -0.224,0.224, step 1, values float32  
Opened (LIVE) 2mFo-DFc_smooth_27 as #1.1.1.4, grid size 96,70,72, pixel
0.355,0.357,0.363, shown at level 0.515, step 1, values float32  
Opened (STATIC) F_calc, phase_calc as #1.1.1.5, grid size 96,70,72, pixel
0.355,0.357,0.363, shown at level -1.27,1.27, step 1, values float32  
3mvs title:  
Structure of the N-terminus of Cadherin 23 [more info...]  
  
Chain information for 3mvs  
---  
Chain | Description | UniProt  
1.2/A | Cadherin-23 | CAD23_MOUSE  
  
Non-standard residues in 3mvs #1.2  
---  
CA — calcium ion  
EDO — 1,2-ethanediol (ethylene glycol)  
  

> close #1

Deleting Crystallographic maps (3mvs-sf.cif)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_smooth_27  

> open 6tqd structureFactors true

Summary of feedback from opening 6tqd fetched from pdb  
---  
warning | WARNING: multiple experimental reflection datasets found:  
F_meas_au, F_meas_sigma_au,  
pdbx_F_plus, pdbx_F_plus_sigma, pdbx_F_minus, pdbx_F_minus_sigma,  
pdbx_anom_difference, pdbx_anom_difference_sigma,  
intensity_meas, intensity_sigma,  
pdbx_I_plus, pdbx_I_plus_sigma, pdbx_I_minus, pdbx_I_minus_sigma  
Automatically choosing "F_meas_au, F_meas_sigma_au".  
notes | Fetching compressed mmCIF 6tqd from
http://files.rcsb.org/download/6tqd.cif  
Fetching CCD BR from http://ligand-expo.rcsb.org/reports/B/BR/BR.cif  
Fetching CCD PG4 from http://ligand-expo.rcsb.org/reports/P/PG4/PG4.cif  
Fetching compressed 6tqd structure factors from
http://files.rcsb.org/download/6tqd-sf.cif  
Resolution: 1.4791831259859027  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 70,66,52, pixel
0.467,0.455,0.49, shown at level 1.16, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 70,66,52, pixel 0.467,0.455,0.49,
shown at level -0.252,0.252, step 1, values float32  
Opened (LIVE) 2mFo-DFc_smooth_23 as #1.1.1.4, grid size 70,66,52, pixel
0.467,0.455,0.49, shown at level 0.67, step 1, values float32  
6tqd title:  
D00-D0 domain of Intimin [more info...]  
  
Chain information for 6tqd  
---  
Chain | Description | UniProt  
1.2/A 1.2/B 1.2/C 1.2/D 1.2/E 1.2/F | Intimin | EAE_ECO27  
  
Non-standard residues in 6tqd #1.2  
---  
BR — bromide ion  
CL — chloride ion  
NA — sodium ion  
PG4 — tetraethylene glycol  
  
6tqd mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
3| author_defined_assembly  
4| author_defined_assembly  
5| author_defined_assembly  
6| author_defined_assembly  
  

> isolde start

> set selectionWidth 4

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 297, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\cmd\cmd.py", line 29, in isolde_start  
get_singleton(session)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\cmd\cmd.py", line 20, in get_singleton  
return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=create)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 193, in get_singleton  
tinst = tool_class(session, tool_name, **kw)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\tool.py", line 186, in __init__  
self.isolde = isolde.Isolde(self)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 317, in __init__  
self._start_gui(gui)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 482, in _start_gui  
self._update_model_list(None, None, force=True)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 1042, in _update_model_list  
self._change_selected_model(model=current_model)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 2513, in _change_selected_model  
m.delete_alt_locs()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1590, in delete_alt_locs  
f = c_function('structure_delete_alt_locs', args =
(ctypes.c_void_p,))(self._c_pointer)  
OSError: exception: access violation reading 0x0000000000000014  
  
OSError: exception: access violation reading 0x0000000000000014  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1590, in delete_alt_locs  
f = c_function('structure_delete_alt_locs', args =
(ctypes.c_void_p,))(self._c_pointer)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 471.11
OpenGL renderer: NVIDIA GeForce RTX 2080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Notebook                        
Model: P7xxTM1
OS: Microsoft Windows 10 Education (Build 19041)
Memory: 68,654,501,888
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz
OSLanguage: en-GB
Locale: ('en_GB', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
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    ChimeraX-AddH: 2.1.10
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[Eric Pettersen]

Using the daily build on my Mac at home, Structure.delete_alt_locs() works for both 1a0m and 5yd4. The *could* be a ctypes problem. Anyway, I need to try it in the daily build on Windows and see what happens.

[Eric Pettersen]

I do get this error with 5yd4 on Windows, but not 1a0m. I don't get the error if I go through residue by residue and call clean_alt_locs().

[Eric Pettersen]

alt loc ANISOU info was being used after the altloc map had been cleared, which will work 99% of the time...