Context Navigation

← Previous Ticket
Next Ticket →

#4625 closed defect (duplicate)

MatchMaker specific chain-chain pairing: wrapped C/C++ object of type ChainMenuButton has been deleted

Reported by:	chimerax-bug-report@…	Owned by:	Eric Pettersen
Priority:	normal	Milestone:
Component:	Structure Comparison	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Linux-5.4.115-1.el8.elrepo.x86_64-x86_64-with-glibc2.14
ChimeraX Version: 1.2 (2021-04-27 05:33:30 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2 (2021-04-27)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /yonath_group/disha/Giardia_DH_AR_AB/30S_FR_GL_postprocess_masked.mrc

Opened 30S_FR_GL_postprocess_masked.mrc as #1, grid size 320,320,320, pixel
0.85, shown at level 0.0334, step 2, values float32  

> close

> open
> /yonath_group/disha/Giardia_DH_AR_AB/Chimera/comparision/new_models/E_coli_7k00.pdb

Chain information for E_coli_7k00.pdb #1  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

> select #1

149338 atoms, 154090 bonds, 1515 pseudobonds, 17719 residues, 3 models
selected  

> show sel cartoons

> hide sel atoms

> color (#!1 & sel) cornflower blue

> select clear

> set bgColor white

> select #1

149338 atoms, 154090 bonds, 1515 pseudobonds, 17719 residues, 3 models
selected  

> ui tool show "Color Actions"

> color sel light sky blue

> select clear

> open
> /yonath_group/disha/Giardia_DH_AR_AB/Chimera/comparision/new_models/human_4ug0.pdb

Summary of feedback from opening
/yonath_group/disha/Giardia_DH_AR_AB/Chimera/comparision/new_models/human_4ug0.pdb  
---  
warnings | Cannot find LINK/SSBOND residue MG (5148 )  
Cannot find LINK/SSBOND residue MG (5102 )  
Cannot find LINK/SSBOND residue MG (5103 )  
Cannot find LINK/SSBOND residue MG (5103 )  
Cannot find LINK/SSBOND residue MG (5104 )  
250 messages similar to the above omitted  
  
Chain information for human_4ug0.pdb #2  
---  
Chain | Description  
2 | No description available  
5 | No description available  
6 | No description available  
7 | No description available  
8 | No description available  
LA | No description available  
LB | No description available  
LC | No description available  
LD | No description available  
LE | No description available  
LF | No description available  
LG | No description available  
LH | No description available  
LI | No description available  
LJ | No description available  
LL | No description available  
LM | No description available  
LN | No description available  
LO | No description available  
LP | No description available  
LQ | No description available  
LR | No description available  
LS | No description available  
LT | No description available  
LU | No description available  
LV | No description available  
LW | No description available  
LX | No description available  
LY | No description available  
LZ | No description available  
La | No description available  
Lb | No description available  
Lc | No description available  
Ld | No description available  
Le | No description available  
Lf | No description available  
Lg | No description available  
Lh | No description available  
Li | No description available  
Lj | No description available  
Lk | No description available  
Ll | No description available  
Lm | No description available  
Ln | No description available  
Lo | No description available  
Lp | No description available  
Lr | No description available  
Lz | No description available  
SA | No description available  
SB | No description available  
SC | No description available  
SD | No description available  
SE | No description available  
SF | No description available  
SG | No description available  
SH | No description available  
SI | No description available  
SJ | No description available  
SK | No description available  
SL | No description available  
SM | No description available  
SN | No description available  
SO | No description available  
SP | No description available  
SQ | No description available  
SR | No description available  
SS | No description available  
ST | No description available  
SU | No description available  
SV | No description available  
SW | No description available  
SX | No description available  
SY | No description available  
SZ | No description available  
Sa | No description available  
Sb | No description available  
Sc | No description available  
Sd | No description available  
Se | No description available  
Sf | No description available  
Sg | No description available  
  

> select #2

218776 atoms, 234831 bonds, 269 pseudobonds, 17789 residues, 3 models selected  

> show sel cartoons

> hide sel atoms

> color sel pale green

> color sel aquamarine

> color sel pale turquoise

> color sel sea green

> color sel medium sea green

> color sel forest green

> color sel lime green

> color sel spring green

> color sel lawn green

> color sel lawn green

> color sel chartreuse

> color sel lime

> color sel light green

> select clear

> select #2

218776 atoms, 234831 bonds, 269 pseudobonds, 17789 residues, 3 models selected  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,2.7149,0,1,0,3.18,0,0,1,2.9332

> select clear

> undo

> undo

> undo

> undo

> open
> /yonath_group/disha/Giardia_DH_AR_AB/Final_model_map/60s_GL_afterRS12_aligned_new_map_real_space_refined.pdb

Chain information for 60s_GL_afterRS12_aligned_new_map_real_space_refined.pdb
#3  
---  
Chain | Description  
1 | No description available  
3 | No description available  
4 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
o | No description available  
p | No description available  
  

> select #3

104108 atoms, 111779 bonds, 96 pseudobonds, 8479 residues, 2 models selected  

> show sel cartoons

> hide sel atoms

> color sel light gray

> color sel hot pink

> color sel orchid

> select clear

> open
> /yonath_group/disha/Giardia_DH_AR_AB/Final_model_map/Giardia_SSU_real_space_refined.pdb

Chain information for Giardia_SSU_real_space_refined.pdb #4  
---  
Chain | Description  
2 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
n | No description available  
  

> select #4

58253 atoms, 62084 bonds, 98 pseudobonds, 5116 residues, 2 models selected  

> show sel cartoons

> hide sel atoms

> color sel orchid

> select clear

> hide #!1 models

> hide #!2 models

> select #3

104108 atoms, 111779 bonds, 96 pseudobonds, 8479 residues, 2 models selected  

> select #4

58253 atoms, 62084 bonds, 98 pseudobonds, 5116 residues, 2 models selected  

> color sel light gray

> select #3

104108 atoms, 111779 bonds, 96 pseudobonds, 8479 residues, 2 models selected  

> color sel light gray

> select clear

> select #2/L8 add #3/3

Expected a keyword  

> select #2/L8

Nothing selected  

> show #!2 models

> select #2/L8

Nothing selected  

> select #2/C

Nothing selected  

> select #2/L8

Nothing selected  

> select #3/3

2501 atoms, 2797 bonds, 117 residues, 1 model selected  

> select ~sel

527974 atoms, 559987 bonds, 1978 pseudobonds, 48986 residues, 10 models
selected  

> hide sel & #!2-4 cartoons

> color (#!2-4 & sel) red

> undo

> select #3/3

2501 atoms, 2797 bonds, 117 residues, 1 model selected  

> color sel orange red

> select clear

> select #2/L8

Nothing selected  

> select #2/C[auth L8]

Expected a keyword  

> select #2/8

3316 atoms, 3700 bonds, 158 residues, 1 model selected  

> hide sel cartoons

> hide sel cartoons

> show sel cartoons

> ui tool show "Show Sequence Viewer"

> select #2/8 showseq

Expected a keyword  

> sequence chain #2/8

Alignment identifier is 2/8  

> select #3/4

2958 atoms, 3304 bonds, 2 pseudobonds, 138 residues, 2 models selected  

> show sel cartoons

> view matrix models #3,1,0,0,-9.893,0,1,0,31.869,0,0,1,-37.436

> undo

> select #2

218776 atoms, 234831 bonds, 269 pseudobonds, 17789 residues, 3 models selected  

> select #3

104108 atoms, 111779 bonds, 96 pseudobonds, 8479 residues, 2 models selected  

> select #3/3

2501 atoms, 2797 bonds, 117 residues, 1 model selected  

> hide sel cartoons

> view matrix models #3,1,0,0,3.2939,0,1,0,-4.6715,0,0,1,-3.6376

> undo

> select #2

218776 atoms, 234831 bonds, 269 pseudobonds, 17789 residues, 3 models selected  

> ~select #2

Nothing selected  

> select #2

218776 atoms, 234831 bonds, 269 pseudobonds, 17789 residues, 3 models selected  

> select #3

104108 atoms, 111779 bonds, 96 pseudobonds, 8479 residues, 2 models selected  

> select add #3/4

104108 atoms, 111779 bonds, 96 pseudobonds, 8479 residues, 2 models selected  

> select #3/4

2958 atoms, 3304 bonds, 2 pseudobonds, 138 residues, 2 models selected  

> select add #2/8

6274 atoms, 7004 bonds, 2 pseudobonds, 296 residues, 3 models selected  

> view matrix models
> #2,1,0,0,-0.64445,0,1,0,0.85281,0,0,1,0.91545,#3,1,0,0,-0.64445,0,1,0,0.85281,0,0,1,0.91545

> view matrix models
> #2,1,0,0,24.395,0,1,0,6.9243,0,0,1,-9.1585,#3,1,0,0,24.395,0,1,0,6.9243,0,0,1,-9.1585

> ui tool show Matchmaker

> matchmaker #!2 to #3/4 & sel pairing bs showAlignment true

Reference chain (60s_GL_afterRS12_aligned_new_map_real_space_refined.pdb (#3)
chain 4) not compatible with BLOSUM-62 similarity matrix  

> ui tool show Matchmaker

> matchmaker #!2 to #3/4 pairing bs matrix Nucleic showAlignment true

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
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 60s_GL_afterRS12_aligned_new_map_real_space_refined.pdb, chain 4
(#3) with human_4ug0.pdb, chain 2 (#2), sequence alignment score = 1.4  
Alignment identifier is 1  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1: human_4ug0.pdb #2/2,
60s_GL_afterRS12_aligned_new_map_real_space_refined.pdb #3/4  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 3 pruned atom pairs is 1.151 angstroms; (across all 7 pairs:
6.517)  
  

> view matrix models
> #2,0.61444,-0.7756,0.14459,126.33,0.21915,-0.0082704,-0.97566,329.56,0.75791,0.63117,0.16489,33.926,#3,1,0,0,10.121,0,1,0,8.583,0,0,1,-8.8646

> view matrix models
> #2,0.61444,-0.7756,0.14459,106.18,0.21915,-0.0082704,-0.97566,324.92,0.75791,0.63117,0.16489,31.251,#3,1,0,0,-10.027,0,1,0,3.9459,0,0,1,-11.539

> select clear

> ui tool show Matchmaker

> matchmaker #2/8 to #3/4 pairing ss matrix Nucleic showAlignment true

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
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 60s_GL_afterRS12_aligned_new_map_real_space_refined.pdb, chain 4
(#3) with human_4ug0.pdb, chain 8 (#2), sequence alignment score = 1.4  
Alignment identifier is 2  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Hiding conservation header for alignment 2  
Chains used in RMSD evaluation for alignment 2: human_4ug0.pdb #2/8,
60s_GL_afterRS12_aligned_new_map_real_space_refined.pdb #3/4  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2  
RMSD between 6 pruned atom pairs is 1.229 angstroms; (across all 7 pairs:
2.148)  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 418.113
OpenGL renderer: Quadro RTX 4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: ASUS
Model: System Product Name
OS: CentOS Stream 8 
Architecture: 64bit ELF
Virutal Machine: none
CPU: 24 AMD Ryzen 9 5900X 12-Core Processor
Cache Size: 512 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           62Gi        13Gi        33Gi       499Mi        16Gi        48Gi
	Swap:          31Gi          0B        31Gi

Graphics:
	05:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU104GL [Quadro RTX 4000] [10de:1eb1] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:12a0]	
	Kernel driver in use: nvidia
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.4.1
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.3
    ChimeraX-AtomicLibrary: 3.1.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.1
    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: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    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: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    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: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.3
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 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: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.7
    distlib: 0.3.1
    distro: 1.5.0
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 1.1.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.2.0

Change History (2)

comment:1 by Eric Pettersen, 5 years ago

Component:	Unassigned → Structure Comparison
Owner:	set to Eric Pettersen
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → MatchMaker specific chain-chain pairing: wrapped C/C++ object of type ChainMenuButton has been deleted

comment:2 by Eric Pettersen, 5 years ago

Resolution:	→ duplicate
Status:	accepted → closed

Note: See TracTickets for help on using tickets.

Download in other formats: