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#10226 assigned defect

Clipper: ArrayMemoryError updating surface

Reported by:	chimerax-bug-report@…	Owned by:	Tristan Croll
Priority:	normal	Milestone:
Component:	Third Party	Version:
Keywords:		Cc:	Tom Goddard
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: access violation

Current thread 0x000020e0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\atomic\ribbon.py", line 501 in vertex_normal_triangle_arrays
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\atomic\ribbon.py", line 191 in _make_ribbon_graphics
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\atomic\ribbon.py", line 589 in compute_ribbons
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\atomic\structure.py", line 600 in _create_ribbon_graphics
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\atomic\structure.py", line 337 in update_graphics_if_needed
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\atomic\structure.py", line 1650 in _update_graphics_if_needed
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\triggerset.py", line 134 in invoke
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\triggerset.py", line 217 in _activate
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\triggerset.py", line 186 in activate
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\triggerset.py", line 354 in activate_trigger
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\view.py", line 271 in check_for_drawing_change
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\updateloop.py", line 65 in draw_new_frame
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\updateloop.py", line 139 in _redraw_timer_callback
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:/Users/Karanbir
> Pahil/OneDrive/Bridge/P31_BFGCADE_NoLPS/P31J421SharpZFlip.mrc"

Opened P31J421SharpZFlip.mrc as #1, grid size 256,256,256, pixel 0.825, shown
at level 0.0679, step 1, values float32  

> volume #1 level 0.1028

> open "C:/Users/Karanbir
> Pahil/OneDrive/Bridge/P31_BFGCADE_NoLPS/Phenix_IM/RealSpaceRefine_51/LptBFGC_real_space_refined_002-coot-15_real_space_refined_051.pdb"

Chain information for
LptBFGC_real_space_refined_002-coot-15_real_space_refined_051.pdb #2  
---  
Chain | Description  
B | No description available  
B2 | No description available  
C | No description available  
F | No description available  
G | No description available  
  

> hide atoms

> show cartoons

> ui tool show ISOLDE

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 100 residues in model #2 to IUPAC-IUB
standards.  
Chain information for
LptBFGC_real_space_refined_002-coot-15_real_space_refined_051.pdb  
---  
Chain | Description  
2.2/B | No description available  
2.2/B2 | No description available  
2.2/C | No description available  
2.2/F | No description available  
2.2/G | No description available  
  
Done loading forcefield  
Opened P31J421SharpZFlip.mrc as #2.1.1.1, grid size 256,256,256, pixel 0.825,
shown at step 1, values float32  

> volume #2.1.1.1 level 0.08641

ISOLDE: stopped sim  

> addh

Summary of feedback from adding hydrogens to
LptBFGC_real_space_refined_002-coot-15_real_space_refined_051.pdb #2.2  
---  
notes | No usable SEQRES records for
LptBFGC_real_space_refined_002-coot-15_real_space_refined_051.pdb (#2.2) chain
B; guessing termini instead  
No usable SEQRES records for
LptBFGC_real_space_refined_002-coot-15_real_space_refined_051.pdb (#2.2) chain
B2; guessing termini instead  
No usable SEQRES records for
LptBFGC_real_space_refined_002-coot-15_real_space_refined_051.pdb (#2.2) chain
C; guessing termini instead  
No usable SEQRES records for
LptBFGC_real_space_refined_002-coot-15_real_space_refined_051.pdb (#2.2) chain
F; guessing termini instead  
No usable SEQRES records for
LptBFGC_real_space_refined_002-coot-15_real_space_refined_051.pdb (#2.2) chain
G; guessing termini instead  
Chain-initial residues that are actual N termini: /B ALA 2, /B2 ALA 2, /C MET
1, /F MET 1, /G GLY 5  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /F LEU 356, /G LYS 359  
Chain-final residues that are not actual C termini: /B PHE 239, /B2 ARG 240,
/C GLU 183  
1019 hydrogen bonds  
/B PHE 239 is not terminus, removing H atom from 'C'  
/B2 ARG 240 is not terminus, removing H atom from 'C'  
/C GLU 183 is not terminus, removing H atom from 'C'  
10950 hydrogens added  
  
ISOLDE: started sim  

> volume #2.1.1.1 level 0.07667

> volume #2.1.1.1 level 0.07017

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> measure buriedarea /A withAtoms2 /D

Buried area between /A and /D = 0  
area /A = 0, area /D = 0, area both = 0  

> clipper spotlight radius 13.00

> clipper spotlight radius 14.00

> clipper spotlight radius 15.00

> clipper spotlight radius 16.00

> clipper spotlight radius 17.00

> clipper spotlight radius 18.00

> clipper spotlight radius 19.00

> clipper spotlight radius 20.00

> volume #2.1.1.1 level 0.08697

> volume #2.1.1.1 level 0.07577

ISOLDE: started sim  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> clipper spotlight radius 5.00

> clipper spotlight radius 50.00

Traceback (most recent call last):  
File "C:\Users\Karanbir Pahil\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 2749, in _start_sim_or_toggle_pause  
self.start_sim()  
File "C:\Users\Karanbir Pahil\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 2804, in start_sim  
sm.start_sim()  
File "C:\Users\Karanbir Pahil\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 677, in start_sim  
sh.start_sim()  
File "C:\Users\Karanbir Pahil\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1606, in start_sim  
self._prepare_sim()  
File "C:\Users\Karanbir Pahil\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1564, in
_prepare_sim  
s = self._simulation = app.Simulation(self.topology, self._system,  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\openmm\app\simulation.py", line 105, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py",
line 4605, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
openmm.OpenMMException: bad allocation  
  
openmm.OpenMMException: bad allocation  
  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py",
line 4605, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\Karanbir Pahil\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 2749, in _start_sim_or_toggle_pause  
self.start_sim()  
File "C:\Users\Karanbir Pahil\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 2804, in start_sim  
sm.start_sim()  
File "C:\Users\Karanbir Pahil\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 677, in start_sim  
sh.start_sim()  
File "C:\Users\Karanbir Pahil\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1606, in start_sim  
self._prepare_sim()  
File "C:\Users\Karanbir Pahil\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1564, in
_prepare_sim  
s = self._simulation = app.Simulation(self.topology, self._system,  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\openmm\app\simulation.py", line 105, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py",
line 4605, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
openmm.OpenMMException: bad allocation  
  
openmm.OpenMMException: bad allocation  
  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py",
line 4605, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
  
See log for complete Python traceback.  
  
ISOLDE: started sim  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Users\Karanbir Pahil\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1168, in
_dihe_r_changed_cb  
self.sim_handler.update_dihedral_restraints(all_changeds)  
File "C:\Users\Karanbir Pahil\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1975, in
update_dihedral_restraints  
force.update_targets(restraints.sim_indices,  
File "C:\Users\Karanbir Pahil\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1371, in
update_targets  
f(int(self.this), n, pointer(ind), pointer(params))  
RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of
range  
  
Error processing trigger "changes":  
RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of
range  
  
File "C:\Users\Karanbir Pahil\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1371, in
update_targets  
f(int(self.this), n, pointer(ind), pointer(params))  
  
See log for complete Python traceback.  
  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Users\Karanbir Pahil\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1168, in
_dihe_r_changed_cb  
self.sim_handler.update_dihedral_restraints(all_changeds)  
File "C:\Users\Karanbir Pahil\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1975, in
update_dihedral_restraints  
force.update_targets(restraints.sim_indices,  
File "C:\Users\Karanbir Pahil\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1371, in
update_targets  
f(int(self.this), n, pointer(ind), pointer(params))  
RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of
range  
  
Error processing trigger "changes":  
RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of
range  
  
File "C:\Users\Karanbir Pahil\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1371, in
update_targets  
f(int(self.this), n, pointer(ind), pointer(params))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Users\Karanbir Pahil\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1168, in
_dihe_r_changed_cb  
self.sim_handler.update_dihedral_restraints(all_changeds)  
File "C:\Users\Karanbir Pahil\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1975, in
update_dihedral_restraints  
force.update_targets(restraints.sim_indices,  
File "C:\Users\Karanbir Pahil\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1371, in
update_targets  
f(int(self.this), n, pointer(ind), pointer(params))  
RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of
range  
  
Error processing trigger "changes":  
RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of
range  
  
File "C:\Users\Karanbir Pahil\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1371, in
update_targets  
f(int(self.this), n, pointer(ind), pointer(params))  
  
See log for complete Python traceback.  
  

> volume #2.1.1.1 level 0.09434

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select clear

ISOLDE: started sim  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> clipper spotlight radius 20.00

> measure buriedarea /A withAtoms2 /D

Buried area between /A and /D = 0  
area /A = 0, area /D = 0, area both = 0  

> select clear

> clipper spotlight radius 25.00

> select clear

ISOLDE: started sim  
Unable to flip peptide bond after 50 rounds. Giving up.  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 9 residues in model #2.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  
ISOLDE: started sim  
Unable to flip peptide bond after 50 rounds. Giving up.  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 14 residues in model #2.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  
ISOLDE: started sim  

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  
ISOLDE: started sim  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> save "C:/Users/Karanbir
> Pahil/OneDrive/Bridge/P31_BFGCADE_NoLPS/Phenix_IM/LptBFGC_real_space_refined_002-coot-15_real_space_refined_051_ISOLDE.pdb"

> close

> open "C:\Users\Karanbir
> Pahil\OneDrive\Bridge\P62_BFGCA\cryosparc_P62_J169_010_volume_map_sharp.mrc"
> format mrc

Opened cryosparc_P62_J169_010_volume_map_sharp.mrc as #1, grid size
320,320,320, pixel 0.825, shown at level 0.0409, step 2, values float32  

> volume #1 step 1

> volume #1 level 0.07464

> volume #1 level 0.1668

> open "C:/Users/Karanbir
> Pahil/OneDrive/Bridge/P62_BFGCA/cryosparc_P62_J100_013_volume_map_sharp
> (2).mrc"

Opened cryosparc_P62_J100_013_volume_map_sharp (2).mrc as #2, grid size
320,320,320, pixel 0.825, shown at level 0.253, step 2, values float32  

> volume #2 step 1

> volume #2 level 0.7419

> volume #1 level 0.1023

> close #1

> open "C:/Users/Karanbir
> Pahil/OneDrive/Bridge/P31_BFGCADE_NoLPS/Phenix_IM/RealSpaceRefine_51/LptBFGC_real_space_refined_002-coot-15_real_space_refined_051.pdb"

Chain information for
LptBFGC_real_space_refined_002-coot-15_real_space_refined_051.pdb #1  
---  
Chain | Description  
B | No description available  
B2 | No description available  
C | No description available  
F | No description available  
G | No description available  
  

> hide #!2 models

> show #!2 models

> select #2

2 models selected  

> ~select #2

Nothing selected  

> select #1

10692 atoms, 10881 bonds, 1371 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.11525,-0.88044,-0.45994,285.45,0.34647,-0.46958,0.81207,29.466,-0.93095,-0.065761,0.35917,192.92

> view matrix models
> #1,-0.047571,-0.96154,-0.2705,266.03,0.3996,-0.26651,0.87709,-5.7724,-0.91545,-0.066368,0.39691,187.13

> ui mousemode right "translate selected atoms"

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.086127,-0.99525,-0.045276,243.8,0.37044,-0.074177,0.92589,-26.222,-0.92486,0.062973,0.37507,179.41

> view matrix models
> #1,-0.14419,-0.98817,-0.052143,251.43,0.37379,-0.10318,0.92176,-23.438,-0.91624,0.11342,0.38425,172.47

> ui mousemode right "translate selected atoms"

> fitmap #1 inMap #2

Fit molecule LptBFGC_real_space_refined_002-coot-15_real_space_refined_051.pdb
(#1) to map cryosparc_P62_J100_013_volume_map_sharp (2).mrc (#2) using 10692
atoms  
average map value = 0.297, steps = 240  
shifted from previous position = 1.45  
rotated from previous position = 10.9 degrees  
atoms outside contour = 8659, contour level = 0.74195  
  
Position of LptBFGC_real_space_refined_002-coot-15_real_space_refined_051.pdb
(#1) relative to cryosparc_P62_J100_013_volume_map_sharp (2).mrc (#2)
coordinates:  
Matrix rotation and translation  
-0.12913900 -0.97243263 -0.19415948 267.28505226  
0.23944459 -0.22058432 0.94552042 -1.11395981  
-0.96228344 0.07561312 0.26132977 196.24559669  
Axis -0.51844532 0.45778472 0.72225176  
Axis point 204.95313566 38.29726615 0.00000000  
Rotation angle (degrees) 122.96979091  
Shift along axis 2.65608946  
  

> fitmap #1 inMap #2

Fit molecule LptBFGC_real_space_refined_002-coot-15_real_space_refined_051.pdb
(#1) to map cryosparc_P62_J100_013_volume_map_sharp (2).mrc (#2) using 10692
atoms  
average map value = 0.9667, steps = 224  
shifted from previous position = 1.71  
rotated from previous position = 2.59 degrees  
atoms outside contour = 6045, contour level = 0.74195  
  
Position of LptBFGC_real_space_refined_002-coot-15_real_space_refined_051.pdb
(#1) relative to cryosparc_P62_J100_013_volume_map_sharp (2).mrc (#2)
coordinates:  
Matrix rotation and translation  
-0.10462408 -0.98198101 -0.15737567 261.12277726  
0.24467246 -0.17879593 0.95297818 -5.48824490  
-0.96394460 0.06119897 0.25897007 199.16070180  
Axis -0.51916973 0.46956261 0.71412446  
Axis point 205.90094331 36.45547514 0.00000000  
Rotation angle (degrees) 120.81214792  
Shift along axis 4.08141295  
  

> ~select #1

Nothing selected  

> volume #2 level 0.5641

> save "C:/Users/Karanbir
> Pahil/OneDrive/Bridge/P62_BFGCA/Starting_P62J100_bfgca_trie.pdb"

> volume #2 level 1.142

> volume #2 level 0.8309

> volume #2 level 0.6975

No model chosen to save relative to  

> save "C:/Users/Karanbir
> Pahil/OneDrive/Bridge/P62_BFGCA/Starting_P62J100_bfgca_trie.pdb" relModel #2

> close #2

> close

> open "C:\Users\Karanbir
> Pahil\OneDrive\Bridge\P62_BFGCA\cryosparc_P62_J169_010_volume_map_sharp.mrc"
> format mrc

Opened cryosparc_P62_J169_010_volume_map_sharp.mrc as #1, grid size
320,320,320, pixel 0.825, shown at level 0.0409, step 2, values float32  

> open "C:/Users/Karanbir
> Pahil/OneDrive/Bridge/P62_BFGCA/Starting_P62J100_bfgca_trie.pdb"

Chain information for Starting_P62J100_bfgca_trie.pdb #2  
---  
Chain | Description  
B | No description available  
B2 | No description available  
C | No description available  
F | No description available  
G | No description available  
  

> volume #1 level 0.07933

> volume #1 step 1

> hide #2 models

> volume #1 level 0.1285

> open "C:/Users/Karanbir
> Pahil/OneDrive/Bridge/P62_BFGCA/cryosparc_P62_J169_010_volume_map.mrc"

Opened cryosparc_P62_J169_010_volume_map.mrc as #3, grid size 320,320,320,
pixel 0.825, shown at level 0.0361, step 2, values float32  

> volume #3 step 1

> volume #3 level 0.04509

> show #!1 models

> hide #!1 models

> show #2 models

> hide atoms

> show cartoons

> close #1

> ui tool show ISOLDE

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 100 residues in model #2 to IUPAC-IUB
standards.  
Chain information for Starting_P62J100_bfgca_trie.pdb  
---  
Chain | Description  
1.2/B | No description available  
1.2/B2 | No description available  
1.2/C | No description available  
1.2/F | No description available  
1.2/G | No description available  
  
Done loading forcefield  
Opened cryosparc_P62_J169_010_volume_map.mrc as #1.1.1.1, grid size
320,320,320, pixel 0.825, shown at step 1, values float32  

> volume #1.1.1.1 level 0.0531

> clipper spotlight radius 6.00

> clipper spotlight radius 60.00

> select clear

ISOLDE: stopped sim  

> addh

Summary of feedback from adding hydrogens to Starting_P62J100_bfgca_trie.pdb
#1.2  
---  
notes | No usable SEQRES records for Starting_P62J100_bfgca_trie.pdb (#1.2)
chain B; guessing termini instead  
Termini for Starting_P62J100_bfgca_trie.pdb (#1.2) chain B2 determined from
SEQRES records  
No usable SEQRES records for Starting_P62J100_bfgca_trie.pdb (#1.2) chain C;
guessing termini instead  
No usable SEQRES records for Starting_P62J100_bfgca_trie.pdb (#1.2) chain F;
guessing termini instead  
No usable SEQRES records for Starting_P62J100_bfgca_trie.pdb (#1.2) chain G;
guessing termini instead  
Chain-initial residues that are actual N termini: /B ALA 2, /B2 ALA 2, /C MET
1, /F MET 1, /G GLY 5, /F MET 1, /G GLY 5, /B ALA 2, /C MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /B2 ARG 240, /F LEU 356, /G
LYS 359, /F LEU 356, /G LYS 359, /B PHE 239, /C GLU 183  
Chain-final residues that are not actual C termini: /B PHE 239, /C GLU 183  
Missing OXT added to C-terminal residue /B2 ARG 240  
Missing OXT added to C-terminal residue /B PHE 239  
Missing OXT added to C-terminal residue /C GLU 183  
1019 hydrogen bonds  
10950 hydrogens added  
  
ISOLDE: started sim  

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 31 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\map\volume.py", line 4010, in _update_drawings  
v.update_drawings()  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\map\volume.py", line 782, in update_drawings  
self._update_surfaces()  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\map\volume.py", line 805, in _update_surfaces  
s.update_surface(ro)  
File "C:\Users\Karanbir Pahil\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\maps\map_handler_base.py", line 194, in
update_surface  
sct.start_compute, (numpy.asfortranarray(v.matrix()), level, det,
vertex_transform.matrix, normal_transform.matrix, False, True),  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 11.7 MiB for an
array with shape (145, 145, 146) and data type float32  
  
Error processing trigger "graphics update":  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 11.7 MiB for an
array with shape (145, 145, 146) and data type float32  
  
File "C:\Users\Karanbir Pahil\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\maps\map_handler_base.py", line 194, in
update_surface  
sct.start_compute, (numpy.asfortranarray(v.matrix()), level, det,
vertex_transform.matrix, normal_transform.matrix, False, True),  
  
See log for complete Python traceback.  
  


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 528.79
OpenGL renderer: NVIDIA GeForce GTX 1050/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: XPS 15 9560
OS: Microsoft Windows 10 Home (Build 19045)
Memory: 17,024,618,496
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-7700HQ CPU @ 2.80GHz
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.3
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 228
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 2 years ago

Cc:	Tom Goddard added
Component:	Unassigned → Third Party
Owner:	set to Tristan Croll
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Clipper: ArrayMemoryError updating surface

May be an old version

comment:2 by Tristan Croll, 2 years ago

Looks like they just ran out of memory (both on the GPU earlier when trying
to start a simulation - the GTX 1050 only had 2GB RAM, then system memory
at the end). Not much that can be done about that.

On Mon, 27 Nov 2023 at 18:44, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

>
>
>
>

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