Probable memory corruption

[philipp.milkereit@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 1.1.dev202007010013 (2020-07-01 00:13:18 UTC)
Description
This refers to a previously submitted Bug report, here with a simpler way to provoke the error:
open 6fai
Drag select in the GUI a large square in the model
delete sel

Log:
> runscript P:\Python\ChimeraXPython\Main.py

> alias restart runscript P:\Python\ChimeraXPython\Main.py $*

> alias +info runscript P:\Python\ChimeraXPython\Info.py 1 2
> Sc_coordinates_semik.csv Compositions_semik.csv

> alias fhelix runscript P:\Python\ChimeraXPython\SearchHelix.py 1
> Sc_coordinates_semik.csv $*

> alias -del runscript P:\Python\ChimeraXPython\Backup.py 1 2 backup 50;
> delete sel

> alias +residue runscript P:\Python\ChimeraXPython\MoveResidue.py 1 2
> Compositions_semik.csv

> alias -residue runscript P:\Python\ChimeraXPython\MoveResidue.py 1 3
> Compositions_semik.csv

> alias +move runscript P:\Python\ChimeraXPython\MoveResidue.py 1 0
> Compositions_semik.csv

> alias -move runscript P:\Python\ChimeraXPython\MoveResidue.py 1 1
> Compositions_semik.csv

> alias +grafik runscript P:\Python\ChimeraXPython\Grafik.py 1 2
> Compositions_semik.csv

> alias +extract crossfade 10; runscript P:\Python\ChimeraXPython\Extract.py 1
> 2; wait 10

> alias -extract crossfade 10; runscript P:\Python\ChimeraXPython\Unextract.py
> 1 2; wait 10

> alias +helix runscript P:\Python\ChimeraXPython\NextHelix.py 1 0
> Sc_coordinates_semik.csv

> alias ++helix runscript P:\Python\ChimeraXPython\NextHelix.py 1 1
> Sc_coordinates_semik.csv

> alias +secstr runscript P:\Python\ChimeraXPython\NextSecStrElement.py 1
> Compositions_semik.csv 0

> alias ++secstr runscript P:\Python\ChimeraXPython\NextSecStrElement.py 1
> Compositions_semik.csv 1

> alias -secstr runscript P:\Python\ChimeraXPython\NextSecStrElement.py 1
> Compositions_semik.csv 2

> alias Backup runscript P:\Python\ChimeraXPython\Backup.py 1 2 backup 50

> alias Restore runscript P:\Python\ChimeraXPython\Restore.py 1 backup

> alias Log log metadata #1

> alias +protein runscript P:\Python\ChimeraXPython\NextProtein.py 1
> Compositions_semik.csv

> alias +SetDomain runscript P:\Python\ChimeraXPython\SetLSUdomains.py 1
> Sc_coordinates_semik.csv $*

> alias NextProteinUnx crossfade 10; runscript
> P:\Python\ChimeraXPython\Unextract.py 1 2; wait 10; runscript
> P:\Python\ChimeraXPython\NextProtein.py 1 Compositions_semik.csv; crossfade
> 1; runscript P:\Python\ChimeraXPython\Extract.py 1 2; wait 40

> alias NextHelixUnx crossfade 10; runscript
> P:\Python\ChimeraXPython\Unextract.py 1 2; wait 10; runscript
> P:\Python\ChimeraXPython\NextHelix.py 1 0 Sc_coordinates_semik.csv;
> crossfade 1; runscript P:\Python\ChimeraXPython\Extract.py 1 2; wait 40

> alias +fitmap fitmap sel inMap #2 moveWholeMolecules 0 search 0 listFits 0

> alias -fitmap runscript P:\Python\ChimeraXPython\FitUndo.py 1

> alias --fitmap runscript P:\Python\ChimeraXPython\FitUndo.py -1

> alias +add runscript P:\Python\ChimeraXPython\SelectModus.py 1

> alias +sub runscript P:\Python\ChimeraXPython\SelectModus.py 2

> alias +rep runscript P:\Python\ChimeraXPython\SelectModus.py 0

> buttonpanel General

> buttonpanel General add Std-Grafik command +grafik row 1 column 1

> buttonpanel General add Xtract+(2step) command +extract row 2 column 1

> buttonpanel General add Xtract-(2step) command -extract row 3 column 1

> buttonpanel General add -------- command Log row 4 column 1

> buttonpanel General add Fit-Local command +fitmap row 5 column 1

> buttonpanel General add Fit-Undo command -fitmap row 6 column 1

> buttonpanel General add Fit-Redo command --fitmap row 7 column 1

> buttonpanel General add -------- command Log row 8 column 1

> buttonpanel General add UnX-NxtProt-X command NextProteinUnx row 9 column 1

> buttonpanel General add -------- command Log row 10 column 1

> buttonpanel General add NxtProtStr command +secstr row 11 column 1

> buttonpanel General add AddProtStr command ++secstr row 12 column 1

> buttonpanel General add RmvProtStr command -secstr row 13 column 1

> buttonpanel General add -------- command Log row 14 column 1

> buttonpanel General add Residue+ command +residue row 15 column 1

> buttonpanel General add Residue- command -residue row 16 column 1

> buttonpanel General add Move+ command +move row 17 column 1

> buttonpanel General add Move- command -move row 18 column 1

> buttonpanel General add -------- command Log row 19 column 1

> buttonpanel General add Backup! command Backup row 20 column 1

> buttonpanel General add restore command Restore row 21 column 1

> buttonpanel LSU-RNA

> buttonpanel LSU-RNA add UnX-NxtHlx-X command NextHelixUnx row 1 column 1

> buttonpanel LSU-RNA add -------- command Log row 2 column 1

> buttonpanel LSU-RNA add NxtRNAHelix command +helix row 3 column 1

> buttonpanel LSU-RNA add NxtRNAHelix+ command ++helix row 4 column 1

> buttonpanel LSU-RNA add -------- command Log row 5 column 1

> buttonpanel LSU-RNA add Domain-0 command "+SetDomain 0" row 6 column 1

> buttonpanel LSU-RNA add Domain-1 command "+SetDomain 1" row 7 column 1

> buttonpanel LSU-RNA add Domain-2 command "+SetDomain 2" row 8 column 1

> buttonpanel LSU-RNA add Domain-3 command "+SetDomain 3" row 9 column 1

> buttonpanel LSU-RNA add Domain-4 command "+SetDomain 4" row 10 column 1

> buttonpanel LSU-RNA add Domain-5 command "+SetDomain 5" row 11 column 1

> buttonpanel LSU-RNA add Domain-6 command "+SetDomain 6" row 12 column 1

> buttonpanel LSU-RNA add Domain-7 command "+SetDomain 7" row 13 column 1

> buttonpanel Replace

> buttonpanel Replace add Add command +add row 1 column 1

> buttonpanel Replace add Subtract command +sub row 2 column 1

> buttonpanel Add

> buttonpanel Add add Replace command +rep row 1 column 1

> buttonpanel Add add Subtract command +sub row 2 column 1

> buttonpanel Subtract

> buttonpanel Subtract add Replace command +rep row 1 column 1

> buttonpanel Subtract add Add command +add row 2 column 1

> tool show Replace

> tool hide Add

> tool hide Subtract

UCSF ChimeraX version: 1.1.dev202007010013 (2020-07-01)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6fai

6fai title:  
Structure of a eukaryotic cytoplasmic pre-40S ribosomal subunit [more info...]  
  
Chain information for 6fai #1  
---  
Chain | Description  
2 | 20S ribosomal RNA  
A | 40S ribosomal protein S0-A  
B | 40S ribosomal protein S1-A  
C | 40S ribosomal protein S2  
D | 40S ribosomal protein S3  
E | 40S ribosomal protein S4-A  
F | 40S ribosomal protein S5  
G | 40S ribosomal protein S6-A  
H | 40S ribosomal protein S7-A  
I | 40S ribosomal protein S8-A  
J | 40S ribosomal protein S9-A  
L | 40S ribosomal protein S11-A  
M | 40S ribosomal protein S12  
N | 40S ribosomal protein S13  
O | 40S ribosomal protein S14-A  
P | 40S ribosomal protein S15  
Q | 40S ribosomal protein S16-A  
R | 40S ribosomal protein S17-A  
S | 40S ribosomal protein S18-A  
T | 40S ribosomal protein S19-A  
U | 40S ribosomal protein S20  
V | 40S ribosomal protein S21-A  
W | 40S ribosomal protein S22-A  
X | 40S ribosomal protein S23-A  
Y | 40S ribosomal protein S24-A  
Z | 40S ribosomal protein S25-A  
b | 40S ribosomal protein S27-A  
c | 40S ribosomal protein S28-A  
d | 40S ribosomal protein S29-A  
e | 40S ribosomal protein S30-A  
g | Guanine nucleotide-binding protein subunit beta-like protein  
h | Pre-rRNA-processing protein PNO1  
i | Essential nuclear protein 1  
j | Protein LTV1  
k | Ribosome biogenesis protein TSR1  
l | Serine/threonine-protein kinase RIO2  
  
Non-standard residues in 6fai #1  
---  
MG — magnesium ion  
ZN — zinc ion  
  
Drag select of 52861 atoms, 1167 pseudobonds  

> delete sel

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1.dev202007010013\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 263, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.1.dev202007010013\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1.dev202007010013\bin\lib\site-
packages\chimerax\std_commands\delete.py", line 22, in delete  
delete_atoms(session, atoms, attached_hyds=attached_hyds)  
File "C:\Program Files\ChimeraX 1.1.dev202007010013\bin\lib\site-
packages\chimerax\std_commands\delete.py", line 39, in delete_atoms  
atoms.delete()  
File "C:\Program Files\ChimeraX 1.1.dev202007010013\bin\lib\site-
packages\chimerax\atomic\molarray.py", line 728, in delete  
args = [ctypes.c_void_p, ctypes.c_size_t])(self._c_pointers, len(self))  
MemoryError: vector<T> too long  
  
MemoryError: vector too long  
  
File "C:\Program Files\ChimeraX 1.1.dev202007010013\bin\lib\site-
packages\chimerax\atomic\molarray.py", line 728, in delete  
args = [ctypes.c_void_p, ctypes.c_size_t])(self._c_pointers, len(self))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 353.50
OpenGL renderer: GeForce GTX 645/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: OptiPlex 9020
OS: Microsoft Windows 10 Education (Build 18363)
Memory: 17,119,232,000
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-4670 CPU @ 3.40GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

[pett]

Added information to ticket #3471