Opened 4 years ago

Closed 4 years ago

Last modified 4 years ago

#5772 closed defect (can't reproduce)

Crash after running MatchMaker

Reported by: chimerax-bug-report@… Owned by: pett
Priority: normal Milestone:
Component: Graphics 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-10-10.0.19042
ChimeraX Version: 1.3rc202112040407 (2021-12-04 04:07:47 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: access violation

Thread 0x00000668 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\threading.py", line 316 in wait
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\threading.py", line 574 in wait
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\threading.py", line 1284 in run
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00001d60 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\multiprocessing\pool.py", line 576 in _handle_results
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00001ccc (most recent call first):
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\multiprocessing\pool.py", line 528 in _handle_tasks
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x000025fc (most recent call first):
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\multiprocessing\connection.py", line 816 in _exhaustive_wait
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\multiprocessing\connection.py", line 884 in wait
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\multiprocessing\pool.py", line 499 in _wait_for_updates
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\multiprocessing\pool.py", line 519 in _handle_workers
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00000dd8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00001850 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003354 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00002e9c (most recent call first):
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x000025c0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x0000262c (most recent call first):
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00001b10 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00001350 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\threading.py", line 930 in _bootstrap

Current thread 0x00003090 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3rc202112040407\bin\lib\runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.3rc202112040407 (2021-12-04)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/Users/mrost/Downloads/6r2w.pdb

6r2w.pdb title:  
Crystal structure of the super-active fviia variant vyt In complex with tissue
factor [more info...]  
  
Chain information for 6r2w.pdb #1  
---  
Chain | Description | UniProt  
H | coagulation factor VII | FA7_HUMAN  
L | coagulation factor VII | FA7_HUMAN  
T | tissue factor | TF_HUMAN  
  

> select /T

3571 atoms, 3362 bonds, 457 residues, 1 model selected  

> coulombic -3,0,3

Expected a keyword  

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue CGU (net charge -2) with am1-bcc method  
Running ANTECHAMBER command: C:/Program Files/ChimeraX
1.3rc202112040407/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\mrost\AppData\Local\Temp\tmp8syww1fj\ante.in.mol2 -fi mol2 -o
C:\Users\mrost\AppData\Local\Temp\tmp8syww1fj\ante.out.mol2 -fo mol2 -c bcc
-nc -2 -j 5 -s 2 -dr n  
(CGU) ``  
(CGU) `Welcome to antechamber 20.0: molecular input file processor.`  
(CGU) ``  
(CGU) `Info: Finished reading file
(C:\Users\mrost\AppData\Local\Temp\tmp8syww1fj\ante.in.mol2); atoms read (29),
bonds read (28).`  
(CGU) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(CGU) `Running: "C:/Program Files/ChimeraX
1.3rc202112040407/bin/amber20/bin/bondtype" -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(CGU) `bash.exe: warning: could not find /tmp, please create!`  
(CGU) ``  
(CGU) ``  
(CGU) `Running: "C:/Program Files/ChimeraX
1.3rc202112040407/bin/amber20/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff`  
(CGU) `bash.exe: warning: could not find /tmp, please create!`  
(CGU) `Info: Total number of electrons: 130; net charge: -2`  
(CGU) ``  
(CGU) `Running: "C:/Program Files/ChimeraX
1.3rc202112040407/bin/amber20/bin/sqm" -O -i sqm.in -o sqm.out`  
(CGU) `bash.exe: warning: could not find /tmp, please create!`  
(CGU) ``  
(CGU) `Running: "C:/Program Files/ChimeraX
1.3rc202112040407/bin/amber20/bin/am1bcc" -i ANTECHAMBER_AM1BCC_PRE.AC -o
ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program Files/ChimeraX
1.3rc202112040407/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1`  
(CGU) `bash.exe: warning: could not find /tmp, please create!`  
(CGU) ``  
(CGU) `Running: "C:/Program Files/ChimeraX
1.3rc202112040407/bin/amber20/bin/atomtype" -f ac -p bcc -o
ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(CGU) `bash.exe: warning: could not find /tmp, please create!`  
(CGU) ``  
Charges for residue CGU determined  
Assigning partial charges to residue CGU+CGU (net charge -4) with am1-bcc
method  
Running ANTECHAMBER command: C:/Program Files/ChimeraX
1.3rc202112040407/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\mrost\AppData\Local\Temp\tmpfjtlfe4z\ante.in.mol2 -fi mol2 -o
C:\Users\mrost\AppData\Local\Temp\tmpfjtlfe4z\ante.out.mol2 -fo mol2 -c bcc
-nc -4 -j 5 -s 2 -dr n  
(CGU+CGU) ``  
(CGU+CGU) `Welcome to antechamber 20.0: molecular input file processor.`  
(CGU+CGU) ``  
(CGU+CGU) `Info: Finished reading file
(C:\Users\mrost\AppData\Local\Temp\tmpfjtlfe4z\ante.in.mol2); atoms read (46),
bonds read (45).`  
(CGU+CGU) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(CGU+CGU) `Running: "C:/Program Files/ChimeraX
1.3rc202112040407/bin/amber20/bin/bondtype" -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(CGU+CGU) `bash.exe: warning: could not find /tmp, please create!`  
(CGU+CGU) ``  
(CGU+CGU) ``  
(CGU+CGU) `Running: "C:/Program Files/ChimeraX
1.3rc202112040407/bin/amber20/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff`  
(CGU+CGU) `bash.exe: warning: could not find /tmp, please create!`  
(CGU+CGU) `Info: Total number of electrons: 220; net charge: -4`  
(CGU+CGU) ``  
(CGU+CGU) `Running: "C:/Program Files/ChimeraX
1.3rc202112040407/bin/amber20/bin/sqm" -O -i sqm.in -o sqm.out`  
(CGU+CGU) `bash.exe: warning: could not find /tmp, please create!`  
Failure running ANTECHAMBER for residue CGU+CGU Check reply log for details  

> select protein

9237 atoms, 9359 bonds, 602 residues, 1 model selected  

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue CGU (net charge -2) with am1-bcc method  
Running ANTECHAMBER command: C:/Program Files/ChimeraX
1.3rc202112040407/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\mrost\AppData\Local\Temp\tmphwh0928n\ante.in.mol2 -fi mol2 -o
C:\Users\mrost\AppData\Local\Temp\tmphwh0928n\ante.out.mol2 -fo mol2 -c bcc
-nc -2 -j 5 -s 2 -dr n  
(CGU) ``  
(CGU) `Welcome to antechamber 20.0: molecular input file processor.`  
(CGU) ``  
(CGU) `Info: Finished reading file
(C:\Users\mrost\AppData\Local\Temp\tmphwh0928n\ante.in.mol2); atoms read (29),
bonds read (28).`  
(CGU) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(CGU) `Running: "C:/Program Files/ChimeraX
1.3rc202112040407/bin/amber20/bin/bondtype" -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(CGU) `bash.exe: warning: could not find /tmp, please create!`  
(CGU) ``  
(CGU) ``  
(CGU) `Running: "C:/Program Files/ChimeraX
1.3rc202112040407/bin/amber20/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff`  
(CGU) `bash.exe: warning: could not find /tmp, please create!`  
(CGU) `Info: Total number of electrons: 130; net charge: -2`  
(CGU) ``  
(CGU) `Running: "C:/Program Files/ChimeraX
1.3rc202112040407/bin/amber20/bin/sqm" -O -i sqm.in -o sqm.out`  
(CGU) `bash.exe: warning: could not find /tmp, please create!`  
Failure running ANTECHAMBER for residue CGU Check reply log for details  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue CGU (net charge -2) with am1-bcc method  
Running ANTECHAMBER command: C:/Program Files/ChimeraX
1.3rc202112040407/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\mrost\AppData\Local\Temp\tmpr1cvkmbg\ante.in.mol2 -fi mol2 -o
C:\Users\mrost\AppData\Local\Temp\tmpr1cvkmbg\ante.out.mol2 -fo mol2 -c bcc
-nc -2 -j 5 -s 2 -dr n  
(CGU) ``  
(CGU) `Welcome to antechamber 20.0: molecular input file processor.`  
(CGU) ``  
(CGU) `Info: Finished reading file
(C:\Users\mrost\AppData\Local\Temp\tmpr1cvkmbg\ante.in.mol2); atoms read (29),
bonds read (28).`  
(CGU) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(CGU) `Running: "C:/Program Files/ChimeraX
1.3rc202112040407/bin/amber20/bin/bondtype" -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(CGU) `bash.exe: warning: could not find /tmp, please create!`  
(CGU) ``  
(CGU) ``  
(CGU) `Running: "C:/Program Files/ChimeraX
1.3rc202112040407/bin/amber20/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff`  
(CGU) `bash.exe: warning: could not find /tmp, please create!`  
(CGU) `Info: Total number of electrons: 130; net charge: -2`  
(CGU) ``  
(CGU) `Running: "C:/Program Files/ChimeraX
1.3rc202112040407/bin/amber20/bin/sqm" -O -i sqm.in -o sqm.out`  
(CGU) `bash.exe: warning: could not find /tmp, please create!`  
Failure running ANTECHAMBER for residue CGU Check reply log for details  

> hide sel atoms

> hide sel cartoons

> show sel cartoons

> select C

3064 atoms, 2428 bonds, 617 residues, 1 model selected  

> select protein

9237 atoms, 9359 bonds, 602 residues, 1 model selected  

> select /T

3571 atoms, 3362 bonds, 457 residues, 1 model selected  

> show sel surfaces

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 6r2w.pdb_T SES surface #1.2: minimum, -15.47, mean -0.69,
maximum 15.56  
To also show corresponding color key, enter the above coulombic command and
add key true  

> coulombic -3:3

Expected a keyword  

> coulombic range -3,3

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue CGU (net charge -2) with am1-bcc method  
Running ANTECHAMBER command: C:/Program Files/ChimeraX
1.3rc202112040407/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\mrost\AppData\Local\Temp\tmp97pk58gd\ante.in.mol2 -fi mol2 -o
C:\Users\mrost\AppData\Local\Temp\tmp97pk58gd\ante.out.mol2 -fo mol2 -c bcc
-nc -2 -j 5 -s 2 -dr n  
(CGU) ``  
(CGU) `Welcome to antechamber 20.0: molecular input file processor.`  
(CGU) ``  
(CGU) `Info: Finished reading file
(C:\Users\mrost\AppData\Local\Temp\tmp97pk58gd\ante.in.mol2); atoms read (29),
bonds read (28).`  
(CGU) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(CGU) `Running: "C:/Program Files/ChimeraX
1.3rc202112040407/bin/amber20/bin/bondtype" -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(CGU) `bash.exe: warning: could not find /tmp, please create!`  
(CGU) ``  
(CGU) ``  
(CGU) `Running: "C:/Program Files/ChimeraX
1.3rc202112040407/bin/amber20/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff`  
(CGU) `bash.exe: warning: could not find /tmp, please create!`  
(CGU) `Info: Total number of electrons: 130; net charge: -2`  
(CGU) ``  
(CGU) `Running: "C:/Program Files/ChimeraX
1.3rc202112040407/bin/amber20/bin/sqm" -O -i sqm.in -o sqm.out`  
(CGU) `bash.exe: warning: could not find /tmp, please create!`  
Failure running ANTECHAMBER for residue CGU Check reply log for details  

> open C:/Users/mrost/Downloads/2ec9.pdb

2ec9.pdb title:  
Crystal structure analysis of human factor viia , souluble tissue factor
complexed with BCX-3607 [more info...]  
  
Chain information for 2ec9.pdb #2  
---  
Chain | Description | UniProt  
H | coagulation factor VII | FA7_HUMAN  
L | coagulation factor VII | FA7_HUMAN  
T | tissue factor | TF_HUMAN  
U | tissue factor | TF_HUMAN  
  

> ui tool show Matchmaker

> matchmaker #!2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6r2w.pdb, chain H (#1) with 2ec9.pdb, chain H (#2), sequence
alignment score = 1251.5  
RMSD between 240 pruned atom pairs is 0.468 angstroms; (across all 249 pairs:
0.993)  
  


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

Log:
UCSF ChimeraX version: 1.3rc202112040407 (2021-12-04)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 462.30
OpenGL renderer: GeForce MX330/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: LENOVO
Model: 82BS
OS: Microsoft Windows 10 Home Single Language (Build 19042)
Memory: 8,415,662,080
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-10210U CPU @ 1.60GHz
OSLanguage: pt-BR
Locale: ('pt_BR', '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-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: 1.3rc202112040407
    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-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 (3)

comment:1 by pett, 4 years ago

Cc: Tom Goddard added
Component: Unassigned → Graphics
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash after running MatchMaker

comment:2 by pett, 4 years ago

Resolution: → can't reproduce
Status: accepted → closed

comment:3 by Tom Goddard, 4 years ago

Crash is in Qt event loop. Who knows if match maker or the earlier coulombic commands had anything to do with it.

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