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Opened 2 years ago
Closed 2 years ago
#9863 closed defect (can't reproduce)
Crash in Qt event loop after opening MRC files, Toolshed check also running
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-5.15.0-70-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x00007f5df3fff640 (most recent call first):
File "/apps/chimerax/1.6.1-jammy/usr/lib/ucsf-chimerax/lib/python3.9/socket.py", line 954 in getaddrinfo
File "/apps/chimerax/1.6.1-jammy/usr/lib/ucsf-chimerax/lib/python3.9/socket.py", line 823 in create_connection
File "/apps/chimerax/1.6.1-jammy/usr/lib/ucsf-chimerax/lib/python3.9/http/client.py", line 946 in connect
File "/apps/chimerax/1.6.1-jammy/usr/lib/ucsf-chimerax/lib/python3.9/http/client.py", line 1447 in connect
File "/apps/chimerax/1.6.1-jammy/usr/lib/ucsf-chimerax/lib/python3.9/http/client.py", line 980 in send
File "/apps/chimerax/1.6.1-jammy/usr/lib/ucsf-chimerax/lib/python3.9/http/client.py", line 1040 in _send_output
File "/apps/chimerax/1.6.1-jammy/usr/lib/ucsf-chimerax/lib/python3.9/http/client.py", line 1280 in endheaders
File "/apps/chimerax/1.6.1-jammy/usr/lib/ucsf-chimerax/lib/python3.9/http/client.py", line 1331 in _send_request
File "/apps/chimerax/1.6.1-jammy/usr/lib/ucsf-chimerax/lib/python3.9/http/client.py", line 1285 in request
File "/apps/chimerax/1.6.1-jammy/usr/lib/ucsf-chimerax/lib/python3.9/urllib/request.py", line 1346 in do_open
File "/apps/chimerax/1.6.1-jammy/usr/lib/ucsf-chimerax/lib/python3.9/urllib/request.py", line 1389 in https_open
File "/apps/chimerax/1.6.1-jammy/usr/lib/ucsf-chimerax/lib/python3.9/urllib/request.py", line 494 in _call_chain
File "/apps/chimerax/1.6.1-jammy/usr/lib/ucsf-chimerax/lib/python3.9/urllib/request.py", line 534 in _open
File "/apps/chimerax/1.6.1-jammy/usr/lib/ucsf-chimerax/lib/python3.9/urllib/request.py", line 517 in open
File "/apps/chimerax/1.6.1-jammy/usr/lib/ucsf-chimerax/lib/python3.9/urllib/request.py", line 214 in urlopen
File "/apps/chimerax/1.6.1-jammy/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/toolshed/available.py", line 49 in load
File "/apps/chimerax/1.6.1-jammy/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/toolshed/__init__.py", line 456 in reload_available
File "/apps/chimerax/1.6.1-jammy/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/apps/chimerax/1.6.1-jammy/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/apps/chimerax/1.6.1-jammy/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x00007f5e6c628740 (most recent call first):
File "/apps/chimerax/1.6.1-jammy/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/apps/chimerax/1.6.1-jammy/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
File "/apps/chimerax/1.6.1-jammy/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/apps/chimerax/1.6.1-jammy/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 87 in _run_code
File "/apps/chimerax/1.6.1-jammy/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /net/kihara/scratch/li3916/CryoLig/datasets/v19_predicted/v19_to_predict/27335/atom_backbone.mrc
> /net/kihara/scratch/li3916/CryoLig/datasets/v19_predicted/v19_to_predict/27335/atom_base.mrc
> /net/kihara/scratch/li3916/CryoLig/datasets/v19_predicted/v19_to_predict/27335/atom_CB.mrc
> /net/kihara/scratch/li3916/CryoLig/datasets/v19_predicted/v19_to_predict/27335/atom_ligand.mrc
> /net/kihara/scratch/li3916/CryoLig/datasets/v19_predicted/v19_to_predict/27335/atom_phosphate.mrc
> /net/kihara/scratch/li3916/CryoLig/datasets/v19_predicted/v19_to_predict/27335/atom_sidechain.mrc
> /net/kihara/scratch/li3916/CryoLig/datasets/v19_predicted/v19_to_predict/27335/atom_sugar.mrc
Opened atom_backbone.mrc as #1.1, grid size 100,118,167, pixel 1, shown at
level 1, step 1, values float32
Opened atom_base.mrc as #1.2, grid size 100,118,167, pixel 1, shown at level
2.14e-10, step 1, values float32
Opened atom_CB.mrc as #1.3, grid size 100,118,167, pixel 1, shown at level
0.335, step 1, values float32
Opened atom_ligand.mrc as #1.4, grid size 100,118,167, pixel 1, shown at level
5e-05, step 1, values float32
Opened atom_phosphate.mrc as #1.5, grid size 100,118,167, pixel 1, shown at
level 1.86e-06, step 1, values float32
Opened atom_sidechain.mrc as #1.6, grid size 100,118,167, pixel 1, shown at
level 1, step 1, values float32
Opened atom_sugar.mrc as #1.7, grid size 100,118,167, pixel 1, shown at level
8.14e-08, step 1, values float32
> open 8dd7
8dd7 title:
The Cryo-EM structure of Drosophila Cryptochrome in complex with Timeless
[more info...]
Chain information for 8dd7 #2
---
Chain | Description | UniProt
A | Methylated-DNA--protein-cysteine methyltransferase,Cryptochrome-1 fusion |
E5BBQ0_HUMAN -188--8, CRY1_DROME 1-520
B | Protein timeless,Methylated-DNA--protein-cysteine methyltransferase fusion
| TIM_DROME 1-1398, E5BBQ0_HUMAN 1406-1582
Non-standard residues in 8dd7 #2
---
FAD — flavin-adenine dinucleotide
> volume #1.1 level 0.5
> volume #1.2 level 0.5
> volume #1.3 level 0.5
> volume #1.4 level 0.5
> volume #1.5 level 0.5
> volume #1.6 level 0.5
> volume #1.7 level 0.5
> color #1.4 #57e389ff models
> transparency 50
> color #1.1 #f9f06bff models
> color #1.1 #99c1f1ff models
> color #1.3 #99c1f1ff models
> color #1.3 #62a0eaff models
> color #1.5 #ffbe6fff models
> color #1.6 #3584e4ff models
> transparency 50
> color #1.7 #ffa348ff models
> color #1.2 #ff7800ff models
> save
> /home/kihara/jain488/CryoLig/CryoEM_Lig/Dataset/v19_analysis/8dd7_27335_all_dens.png
> transparentBackground true
> hide #!1.2 models
> hide #!1.1 models
> hide #!1.3 models
> hide #!1.5 models
> hide #!1.6 models
> hide #!1.7 models
> save
> /home/kihara/jain488/CryoLig/CryoEM_Lig/Dataset/v19_analysis/8dd7_27335_lig_1.png
> transparentBackground true
> save
> /home/kihara/jain488/CryoLig/CryoEM_Lig/Dataset/v19_analysis/8dd7_27335_lig_2.png
> transparentBackground true
> select /A:316
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:139
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:138
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:136
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
52 atoms, 54 bonds, 6 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select /A:110
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
23 atoms, 22 bonds, 3 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select /A:414
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
107 atoms, 112 bonds, 13 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> save
> /home/kihara/jain488/CryoLig/CryoEM_Lig/Dataset/v19_analysis/8dd7_27335_lig_2.png
> transparentBackground true
> save
> /home/kihara/jain488/CryoLig/CryoEM_Lig/Dataset/v19_analysis/8dd7_27335_lig_3.png
> transparentBackground true
> save
> /home/kihara/jain488/CryoLig/CryoEM_Lig/Dataset/v19_analysis/8dd7_27335_lig_4.png
> transparentBackground true
> close #1-2
> open
> /net/kihara/scratch/li3916/CryoLig/datasets/v19_predicted/v19_to_predict/33498/atom_backbone.mrc
> /net/kihara/scratch/li3916/CryoLig/datasets/v19_predicted/v19_to_predict/33498/atom_base.mrc
> /net/kihara/scratch/li3916/CryoLig/datasets/v19_predicted/v19_to_predict/33498/atom_CB.mrc
> /net/kihara/scratch/li3916/CryoLig/datasets/v19_predicted/v19_to_predict/33498/atom_ligand.mrc
> /net/kihara/scratch/li3916/CryoLig/datasets/v19_predicted/v19_to_predict/33498/atom_phosphate.mrc
> /net/kihara/scratch/li3916/CryoLig/datasets/v19_predicted/v19_to_predict/33498/atom_sidechain.mrc
> /net/kihara/scratch/li3916/CryoLig/datasets/v19_predicted/v19_to_predict/33498/atom_sugar.mrc
Opened atom_backbone.mrc as #1.1, grid size 216,195,210, pixel 1, shown at
level 1, step 1, values float32
Opened atom_base.mrc as #1.2, grid size 216,195,210, pixel 1, shown at level
1.25e-05, step 1, values float32
Opened atom_CB.mrc as #1.3, grid size 216,195,210, pixel 1, shown at level
0.23, step 1, values float32
Opened atom_ligand.mrc as #1.4, grid size 216,195,210, pixel 1, shown at level
5e-05, step 1, values float32
Opened atom_phosphate.mrc as #1.5, grid size 216,195,210, pixel 1, shown at
level 1.25e-05, step 1, values float32
Opened atom_sidechain.mrc as #1.6, grid size 216,195,210, pixel 1, shown at
level 1, step 1, values float32
Opened atom_sugar.mrc as #1.7, grid size 216,195,210, pixel 1, shown at level
1.25e-05, step 1, values float32
> open 7xx2
Summary of feedback from opening 7xx2 fetched from pdb
---
note | Fetching compressed mmCIF 7xx2 from
http://files.rcsb.org/download/7xx2.cif
7xx2 title:
Cryo-EM structure of Sr35 resistosome induced by AvrSr35 R381A [more info...]
Chain information for 7xx2 #2
---
Chain | Description | UniProt
A C E G I | CNL9 | S5ABD6_TRIMO 1-919
B | AvrSr35 | A0A5B0N367_PUCGR 26-578
Non-standard residues in 7xx2 #2
---
ATP — adenosine-5'-triphosphate
> hide atoms
> show cartoons
> volume #1.1 level 0.5
> volume #1.2 level 0.5
> volume #1.3 level 0.5
> volume #1.4 level 0.5
> volume #1.5 level 0.5
> volume #1.6 level 0.5
> volume #1.7 level 0.5
> color #1.4 #8ff0a4ff models
> hide #!1.3 models
> show #!1.3 models
> color #1.3 #99c1f1ff models
> color #1.2 #99c1f1ff models
> color #1.2 #ffbe6fff models
> color #1.1 #99c1f1ff models
> color #1.5 #ffbe6fff models
> color #1.6 #99c1f1ff models
> color #1.7 #ffbe6fff models
> hide #!1.5 models
> hide #!1.6 models
> hide #!1.7 models
> hide #!1.3 models
> show #!1.6 models
> show #!1.7 models
> show #!1.5 models
> show #!1.3 models
> transparency 50
> save
> /home/kihara/jain488/CryoLig/CryoEM_Lig/Dataset/v19_analysis/7xx2_33498_whole_all_dens].png
> transparentBackground true
> hide #!1.7 models
> hide #!1.6 models
> hide #!1.5 models
> hide #!1.3 models
> hide #!1.2 models
> hide #!1.1 models
> select ::name="ATP"
155 atoms, 165 bonds, 5 residues, 1 model selected
> show sel atoms
> color #2 #1a5fb4ff
> color #2 #613583ff
> color #2 #a51d2dff
> color #2 #c64600ff
> color #2 #63452cff
> color #2 #9a9996ff
> color #2 black
> color #2 #9a9996ff
> show #!1.7 models
> show #!1.6 models
> show #!1.5 models
> show #!1.3 models
> show #!1.2 models
> show #!1.1 models
> save
> /home/kihara/jain488/CryoLig/CryoEM_Lig/Dataset/v19_analysis/7xx2_33498_whole_all_dens.png
> transparentBackground true
> hide #!1.7 models
> hide #!1.6 models
> hide #!1.5 models
> hide #!1.3 models
> hide #!1.2 models
> hide #!1.1 models
> save
> /home/kihara/jain488/CryoLig/CryoEM_Lig/Dataset/v19_analysis/7xx2_33498_all_lig_1.png
> transparentBackground true
> save
> /home/kihara/jain488/CryoLig/CryoEM_Lig/Dataset/v19_analysis/7xx2_33498_all_lig_2.png
> transparentBackground true
> save
> /home/kihara/jain488/CryoLig/CryoEM_Lig/Dataset/v19_analysis/7xx2_33498_all_lig_3.png
> transparentBackground true
> show #!1.7 models
> show #!1.6 models
> show #!1.5 models
> show #!1.3 models
> show #!1.2 models
> show #!1.1 models
Volume zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 7 maps.
> hide #!1.7 models
> hide #!1.5 models
> hide #!1.3 models
> hide #!1.2 models
> hide #!1.1 models
> hide #!1.4 models
> volume zone #1.6 nearAtoms sel & #2 range 6
> show #!1.4 models
> save
> /home/kihara/jain488/CryoLig/CryoEM_Lig/Dataset/v19_analysis/7xx2_33498_all_lig__sidechain.png
> transparentBackground true
> save
> /home/kihara/jain488/CryoLig/CryoEM_Lig/Dataset/v19_analysis/7xx2_33498_all_lig_sidechain_2.png
> transparentBackground true
> close #1-2
> open
> /net/kihara/scratch/li3916/CryoLig/datasets/v19_predicted/v19_to_predict/10232/atom_backbone.mrc
> /net/kihara/scratch/li3916/CryoLig/datasets/v19_predicted/v19_to_predict/10232/atom_base.mrc
> /net/kihara/scratch/li3916/CryoLig/datasets/v19_predicted/v19_to_predict/10232/atom_CB.mrc
> /net/kihara/scratch/li3916/CryoLig/datasets/v19_predicted/v19_to_predict/10232/atom_ligand.mrc
> /net/kihara/scratch/li3916/CryoLig/datasets/v19_predicted/v19_to_predict/10232/atom_phosphate.mrc
> /net/kihara/scratch/li3916/CryoLig/datasets/v19_predicted/v19_to_predict/10232/atom_sidechain.mrc
> /net/kihara/scratch/li3916/CryoLig/datasets/v19_predicted/v19_to_predict/10232/atom_sugar.mrc
Opened atom_backbone.mrc as #1.1, grid size 154,179,242, pixel 1, shown at
level 1, step 1, values float32
Opened atom_base.mrc as #1.2, grid size 154,179,242, pixel 1, shown at level
6.18e-06, step 1, values float32
Opened atom_CB.mrc as #1.3, grid size 154,179,242, pixel 1, shown at level
0.333, step 1, values float32
Opened atom_ligand.mrc as #1.4, grid size 154,179,242, pixel 1, shown at level
5e-05, step 1, values float32
Opened atom_phosphate.mrc as #1.5, grid size 154,179,242, pixel 1, shown at
level 1.24e-05, step 1, values float32
Opened atom_sidechain.mrc as #1.6, grid size 154,179,242, pixel 1, shown at
level 1, step 1, values float32
Opened atom_sugar.mrc as #1.7, grid size 154,179,242, pixel 1, shown at level
6.26e-06, step 1, values float32
> color #1.4 #8ff0a4ff models
> open 6skz
Summary of feedback from opening 6skz fetched from pdb
---
note | Fetching compressed mmCIF 6skz from
http://files.rcsb.org/download/6skz.cif
6skz title:
Structure of the closed conformation of CtTel1 [more info...]
Chain information for 6skz #2
---
Chain | Description | UniProt
A | Serine/threonine-protein kinase Tel1 | G0S4S9_CHATD 1-2944
Non-standard residues in 6skz #2
---
AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
5'-(3-thiotriphosphate); adenosine 5'-(γ-thiotriphosphate);
adenosine-5'-diphosphate monothiophosphate)
MG — magnesium ion
> transparency 50
> select ::name="AGS"
31 atoms, 33 bonds, 1 residue, 1 model selected
> volume show
> show sel atoms
> volume #1.1 level 0.5
> volume #1.2 level 0.5
> volume #1.3 level 0.5
> volume #1.5 level 0.5
> volume #1.4 level 0.5
> volume #1.6 level 0.5
> volume #1.7 level 0.5
> hide #!1.7 models
> show #!1.7 models
> hide #!1.6 models
> show #!1.6 models
> hide #!1.6 models
> show #!1.6 models
> hide #!1.6 models
> show #!1.6 models
> open 6skz fromDatabase rcsb_bio
Summary of feedback from opening 6skz fetched from rcsb_bio
---
note | Fetching compressed 6skz bioassembly 1 from
https://files.rcsb.org/download/6skz-assembly1.cif
6skz bioassembly 1 title:
Structure of the closed conformation of CtTel1 [more info...]
Chain information for 6skz bioassembly 1 #3
---
Chain | Description
A | Serine/threonine-protein kinase Tel1
Non-standard residues in 6skz bioassembly 1 #3
---
AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
5'-(3-thiotriphosphate); adenosine 5'-(γ-thiotriphosphate);
adenosine-5'-diphosphate monothiophosphate)
MG — magnesium ion
Opened 1 biological assemblies for 6skz
> hide #!2 models
> close #2
> open 10232
'10232' has no suffix
> open 10232 fromDatabase emdb
Summary of feedback from opening 10232 fetched from emdb
---
note | Fetching compressed map 10232 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-10232/map/emd_10232.map.gz
Opened emdb 10232 as #2, grid size 352,352,352, pixel 1.06, shown at level
0.00242, step 2, values float32
> volume #2 level 0.0126
> hide #!2 models
> show #!2 models
> hide #!1.7 models
> hide #!1.6 models
> hide #!1.5 models
> hide #!1.3 models
> hide #!1.2 models
> hide #!1.1 models
> show #!1.7 models
> show #!1.5 models
> show #!1.6 models
> show #!1.3 models
> show #!1.2 models
> show #!1.1 models
> hide #!2 models
> select ::name="AGS"
31 atoms, 33 bonds, 1 residue, 1 model selected
> show sel atoms
> save
> /home/kihara/jain488/CryoLig/CryoEM_Lig/Dataset/v19_analysis/6skz_10232_whole_all_dens.png
> transparentBackground true
> color #1.1 #99c1f1ff models
> color #1.2 #ffbe6fff models
> color #1.3 #99c1f1ff models
> color #1.5 #ffbe6fff models
> color #1.6 #99c1f1ff models
> color #1.7 #ffbe6fff models
> transparency 50
> save
> /home/kihara/jain488/CryoLig/CryoEM_Lig/Dataset/v19_analysis/6skz_10232_whole_all_dens_2.png
> transparentBackground true
> hide #!1.7 models
> hide #!1.6 models
> hide #!1.5 models
> hide #!1.3 models
> hide #!1.2 models
> hide #!1.1 models
> save
> /home/kihara/jain488/CryoLig/CryoEM_Lig/Dataset/v19_analysis/6skz_10232_lig_only_1.png
> transparentBackground true
> save
> /home/kihara/jain488/CryoLig/CryoEM_Lig/Dataset/v19_analysis/6skz_10232_lig_only_2.png
> transparentBackground true
> save
> /home/kihara/jain488/CryoLig/CryoEM_Lig/Dataset/v19_analysis/6skz_10232_lig_only_3.png
> transparentBackground true
> show #!1.1 models
Volume zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 2 maps.
> hide #!1.4 models
> volume zone #1.1 nearAtoms sel & #3 range 6
> show #!1.2 models
> hide #!1.1 models
> show #!1.3 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> volume zone #1.3 nearAtoms sel & #3 range 6
> show #!1.5 models
> hide #!1.3 models
> show #!1.6 models
> hide #!1.5 models
> volume zone #1.6 nearAtoms sel & #3 range 6
> show #!1.3 models
> show #!1.1 models
> show #!1.4 models
> hide #!1.6 models
> show #!1.6 models
> volume #1.3 level 0.5304
> volume #1.3 level 0.5
> hide #!1.6 models
> hide #!1.3 models
> show #!1.3 models
> show #!1.6 models
> volume #1.6 level 0.872
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
20898 atoms, 21306 bonds, 20 pseudobonds, 2638 residues, 2 models selected
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> style sel stick
Changed 20898 atom styles
> show sel atoms
> select clear
> select ::name="AGS"
31 atoms, 33 bonds, 1 residue, 1 model selected
> save
> /home/kihara/jain488/CryoLig/CryoEM_Lig/Dataset/v19_analysis/6skz_10232_lig_prot_zone_4.png
> transparentBackground true
> save
> /home/kihara/jain488/CryoLig/CryoEM_Lig/Dataset/v19_analysis/6skz_10232_lig_prot_zone_5.png
> transparentBackground true
> undo
> select clear
> save
> /home/kihara/jain488/CryoLig/CryoEM_Lig/Dataset/v19_analysis/6skz_10232_lig_prot_zone_6.png
> transparentBackground true
> save
> /home/kihara/jain488/CryoLig/CryoEM_Lig/Dataset/v19_analysis/6skz_10232_lig_prot_zone_7.png
> transparentBackground true
> close #1-3#1.1-7
> open
> /net/kihara/scratch/li3916/CryoLig/datasets/v19_predicted/v19_to_predict/26733/atom_backbone.mrc
> /net/kihara/scratch/li3916/CryoLig/datasets/v19_predicted/v19_to_predict/26733/atom_base.mrc
> /net/kihara/scratch/li3916/CryoLig/datasets/v19_predicted/v19_to_predict/26733/atom_CB.mrc
> /net/kihara/scratch/li3916/CryoLig/datasets/v19_predicted/v19_to_predict/26733/atom_ligand.mrc
> /net/kihara/scratch/li3916/CryoLig/datasets/v19_predicted/v19_to_predict/26733/atom_phosphate.mrc
> /net/kihara/scratch/li3916/CryoLig/datasets/v19_predicted/v19_to_predict/26733/atom_sidechain.mrc
> /net/kihara/scratch/li3916/CryoLig/datasets/v19_predicted/v19_to_predict/26733/atom_sugar.mrc
Opened atom_backbone.mrc as #1.1, grid size 165,166,224, pixel 1, shown at
level 1, step 1, values float32
Opened atom_base.mrc as #1.2, grid size 165,166,224, pixel 1, shown at level
6.25e-06, step 1, values float32
Opened atom_CB.mrc as #1.3, grid size 165,166,224, pixel 1, shown at level
0.462, step 1, values float32
Opened atom_ligand.mrc as #1.4, grid size 165,166,224, pixel 1, shown at level
5e-05, step 1, values float32
Opened atom_phosphate.mrc as #1.5, grid size 165,166,224, pixel 1, shown at
level 6.25e-06, step 1, values float32
Opened atom_sidechain.mrc as #1.6, grid size 165,166,224, pixel 1, shown at
level 1, step 1, values float32
Opened atom_sugar.mrc as #1.7, grid size 165,166,224, pixel 1, shown at level
6.25e-06, step 1, values float32
> open 7usd
Summary of feedback from opening 7usd fetched from pdb
---
note | Fetching compressed mmCIF 7usd from
http://files.rcsb.org/download/7usd.cif
7usd title:
Cryo-EM structure of D-site Rac1-bound WAVE Regulatory Complex [more info...]
Chain information for 7usd #2
---
Chain | Description | UniProt
A | Cytoplasmic FMR1-interacting protein 1 | CYFP1_HUMAN 1-1253
B | Nck-associated protein 1 | NCKP1_HUMAN 1-1128
C | Wiskott-Aldrich syndrome protein family member 1 | WASF1_HUMAN 1-466
485-559
D | Protein BRICK1 | BRK1_HUMAN 1-75
E | Abl interactor 2 | E9PEZ7_HUMAN 1-158
F | Ras-related C3 botulinum toxin substrate 1 | RAC1_HUMAN 1-188
Non-standard residues in 7usd #2
---
GTP — guanosine-5'-triphosphate
MG — magnesium ion
> hide atoms
> show cartoons
> color #1.4 #8ff0a4ff models
> select ::name="GTP"
32 atoms, 34 bonds, 1 residue, 1 model selected
> show sel atoms
> transparency 50
> show sel atoms
> select ::name="GTP"
32 atoms, 34 bonds, 1 residue, 1 model selected
> show sel atoms
> select ::name="MG"
1 atom, 1 residue, 1 model selected
> show sel atoms
> volume #1.1 level 0.5
> volume #1.2 level 0.5
> volume #1.3 level 0.5
> volume #1.4 level 0.5
> volume #1.5 level 0.5
> volume #1.6 level 0.5
> volume #1.7 level 0.5
> color #1.1 #99c1f180 models
> color #1.3 #99c1f180 models
> color #1.6 #99c1f180 models
> color #1.6 #b2b2b280 models
> color #1.3 #b2b2b280 models
> color #1.1 #b2b2b280 models
> save
> /home/kihara/jain488/CryoLig/CryoEM_Lig/Dataset/v19_analysis/7usd_26733_whole_all_dens.png
> transparentBackground true
> save
> /home/kihara/jain488/CryoLig/CryoEM_Lig/Dataset/v19_analysis/7usd_26733_whole_zoom_lig_1.png
> transparentBackground true
> save
> /home/kihara/jain488/CryoLig/CryoEM_Lig/Dataset/v19_analysis/7usd_26733_whole_zoom_lig_2.png
> transparentBackground true
> hide #!1.3 models
> hide #!1.2 models
> hide #!1.1 models
> hide #!1.5 models
> hide #!1.6 models
> hide #!1.7 models
> save
> /home/kihara/jain488/CryoLig/CryoEM_Lig/Dataset/v19_analysis/7usd_26733_whole_zoom_lig_3.png
> transparentBackground true
> close #1-2#1.1-7
> open
> /net/kihara/scratch/li3916/CryoLig/datasets/v19_predicted/v19_to_predict/32761/atom_backbone.mrc
> /net/kihara/scratch/li3916/CryoLig/datasets/v19_predicted/v19_to_predict/32761/atom_base.mrc
> /net/kihara/scratch/li3916/CryoLig/datasets/v19_predicted/v19_to_predict/32761/atom_CB.mrc
> /net/kihara/scratch/li3916/CryoLig/datasets/v19_predicted/v19_to_predict/32761/atom_ligand.mrc
> /net/kihara/scratch/li3916/CryoLig/datasets/v19_predicted/v19_to_predict/32761/atom_phosphate.mrc
> /net/kihara/scratch/li3916/CryoLig/datasets/v19_predicted/v19_to_predict/32761/atom_sidechain.mrc
> /net/kihara/scratch/li3916/CryoLig/datasets/v19_predicted/v19_to_predict/32761/atom_sugar.mrc
Opened atom_backbone.mrc as #1.1, grid size 127,136,155, pixel 1, shown at
level 0.25, step 1, values float32
Opened atom_base.mrc as #1.2, grid size 127,136,155, pixel 1, shown at level
4.17e-06, step 1, values float32
Opened atom_CB.mrc as #1.3, grid size 127,136,155, pixel 1, shown at level
5e-05, step 1, values float32
Opened atom_ligand.mrc as #1.4, grid size 127,136,155, pixel 1, shown at level
5e-05, step 1, values float32
Opened atom_phosphate.mrc as #1.5, grid size 127,136,155, pixel 1, shown at
level 5.87e-11, step 1, values float32
Opened atom_sidechain.mrc as #1.6, grid size 127,136,155, pixel 1, shown at
level 0.589, step 1, values float32
Opened atom_sugar.mrc as #1.7, grid size 127,136,155, pixel 1, shown at level
6.68e-09, step 1, values float32
> open 7wsn from rcsb_pdb
No such database 'rcsb_pdb'
> open 7wsn fromDatabase rcsb_bio
Summary of feedback from opening 7wsn fetched from rcsb_bio
---
notes | Fetching compressed 7wsn bioassembly 1 from
https://files.rcsb.org/download/7wsn-assembly1.cif
Fetching CCD 5RH from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/H/5RH/5RH.cif
7wsn bioassembly 1 title:
Cryo-EM structure of human glucose transporter GLUT4 bound to cytochalasin B
in detergent micelles [more info...]
Chain information for 7wsn bioassembly 1 #2
---
Chain | Description
A | Solute carrier family 2, facilitated glucose transporter member 4
Non-standard residues in 7wsn bioassembly 1 #2
---
5RH — Cytochalasin B
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
Opened 1 biological assemblies for 7wsn
> select ::name="5RH"::name="NAG"
63 atoms, 66 bonds, 3 residues, 1 model selected
> show sel atoms
> color #1.4 #8ff0a4ff models
> volume #1.1 level 0.5
> volume #1.2 level 0.5
> volume #1.3 level 0.5
> volume #1.4 level 0.5
> volume #1.5 level 0.5
> volume #1.6 level 0.5
> volume #1.7 level 0.5
> transparency 50
> select up
3567 atoms, 3649 bonds, 466 residues, 1 model selected
> select down
63 atoms, 66 bonds, 3 residues, 1 model selected
> select down
63 atoms, 66 bonds, 3 residues, 1 model selected
> save
> /home/kihara/jain488/CryoLig/CryoEM_Lig/Dataset/v19_analysis/7wsn_32761_whole_all_dens.png
> transparentBackground true
> hide #!1.5 models
> show #!1.5 models
> save
> /home/kihara/jain488/CryoLig/CryoEM_Lig/Dataset/v19_analysis/7wsn_32761_lig_dens_1.png
> transparentBackground true
> hide #!1.3 models
> hide #!1.2 models
> hide #!1.1 models
> hide #!1.5 models
> hide #!1.6 models
> hide #!1.7 models
> save
> /home/kihara/jain488/CryoLig/CryoEM_Lig/Dataset/v19_analysis/7wsn_32761_lig_dens_2.png
> transparentBackground true
> save
> /home/kihara/jain488/CryoLig/CryoEM_Lig/Dataset/v19_analysis/7wsn_32761_lig_dens_3.png
> transparentBackground true
> save
> /home/kihara/jain488/CryoLig/CryoEM_Lig/Dataset/v19_analysis/7wsn_32761_lig_dens_4.png
> transparentBackground true
> save
> /home/kihara/jain488/CryoLig/CryoEM_Lig/Dataset/v19_analysis/7wsn_32761_lig_dens_5.png
> transparentBackground true
> save
> /home/kihara/jain488/CryoLig/CryoEM_Lig/Dataset/v19_analysis/7wsn_32761_lig_dens_6.png
> transparentBackground true
> close #2#1#1.1-7
> open
> /net/kihara/scratch/li3916/CryoLig/datasets/v19_predicted/v19_to_predict/4577/atom_backbone.mrc
> /net/kihara/scratch/li3916/CryoLig/datasets/v19_predicted/v19_to_predict/4577/atom_base.mrc
> /net/kihara/scratch/li3916/CryoLig/datasets/v19_predicted/v19_to_predict/4577/atom_CB.mrc
> /net/kihara/scratch/li3916/CryoLig/datasets/v19_predicted/v19_to_predict/4577/atom_ligand.mrc
> /net/kihara/scratch/li3916/CryoLig/datasets/v19_predicted/v19_to_predict/4577/atom_phosphate.mrc
> /net/kihara/scratch/li3916/CryoLig/datasets/v19_predicted/v19_to_predict/4577/atom_sidechain.mrc
> /net/kihara/scratch/li3916/CryoLig/datasets/v19_predicted/v19_to_predict/4577/atom_sugar.mrc
Opened atom_backbone.mrc as #1.1, grid size 339,339,339, pixel 1, shown at
level 1, step 2, values float32
Opened atom_base.mrc as #1.2, grid size 339,339,339, pixel 1, shown at level
6.25e-06, step 2, values float32
Opened atom_CB.mrc as #1.3, grid size 339,339,339, pixel 1, shown at level
0.5, step 2, values float32
Opened atom_ligand.mrc as #1.4, grid size 339,339,339, pixel 1, shown at level
5e-05, step 2, values float32
Opened atom_phosphate.mrc as #1.5, grid size 339,339,339, pixel 1, shown at
level 1.88e-05, step 2, values float32
Opened atom_sidechain.mrc as #1.6, grid size 339,339,339, pixel 1, shown at
level 1, step 2, values float32
Opened atom_sugar.mrc as #1.7, grid size 339,339,339, pixel 1, shown at level
1.88e-05, step 2, values float32
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 3.3.0 NVIDIA 470.182.03
OpenGL renderer: NVIDIA GeForce GTX 1080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: System manufacturer
Model: System Product Name
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 8 Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz
Cache Size: 10240 KB
Memory:
total used free shared buff/cache available
Mem: 46Gi 7.5Gi 6.3Gi 139Mi 33Gi 38Gi
Swap: 8.0Gi 3.8Gi 4.2Gi
Graphics:
01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [GeForce GTX 1080 Ti] [10de:1b06] (rev a1)
Subsystem: ASUSTeK Computer Inc. GP102 [GeForce GTX 1080 Ti] [1043:85e5]
Kernel driver in use: nvidia
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2023.5.7
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
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cycler: 0.11.0
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idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
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jupyter-client: 8.0.2
jupyter-core: 5.3.0
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kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
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matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 23.1
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (2)
comment:1 by , 2 years ago
| Component: | Unassigned → Input/Output |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash after opening MRC files |
comment:2 by , 2 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
| Summary: | Crash after opening MRC files → Crash in Qt event loop after opening MRC files, Toolshed check also running |
No clues as to what caused the crash.
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Toolshed load was also running after all that time?