![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 years ago
Closed 2 years ago
#9306 closed defect (duplicate)
"Set" no longer directly in collections module
| Reported by: | Tristan Croll | Owned by: | Eric Pettersen |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-5.19.0-43-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.7.dev202306142048 (2023-06-14 20:48:12 UTC)
Description
Not sure why this only just cropped up now... but it seems `Set` was removed from `collections` in Python 3.10.
Log:
> isolde shorthand
Initialising ISOLDE-specific command aliases:
Alias Equivalent full command
-------------------------------------------------
st isolde step {arguments}
aw isolde add water {arguments}
awsf isolde add water {arguments} sim false
al isolde add ligand {arguments}
aa isolde add aa $1 sel {arguments}
ht isolde mod his sel {arguments}
so setattr sel atoms occupancy {arguments}
ab isolde adjust bfactors {arguments}
ss isolde sim start sel
rt isolde release torsions sel {arguments}
rd isolde release distances sel {arguments}
ra rd; rt
pf isolde pepflip sel
cf isolde cisflip sel
cbb color bfactor {arguments}
cbo color byattr occupancy {arguments}
cbc color {arguments} bychain; color {arguments} byhet
cs clipper set contourSensitivity {arguments}
UCSF ChimeraX version: 1.7.dev202306142048 (2023-06-14)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 8grx
Summary of feedback from opening 8grx fetched from pdb
---
note | Fetching compressed mmCIF 8grx from
http://files.rcsb.org/download/8grx.cif
8grx title:
APOE4 receptor in complex with APOE4 NTD [more info...]
Chain information for 8grx #1
---
Chain | Description | UniProt
A C | Apolipoprotein E | APOE_HUMAN 23-162
B D | Leukocyte immunoglobulin-like receptor subfamily A member 6 |
LIRA6_HUMAN 25-420
> log metadata #1
Metadata for 8grx #1
---
Title | APOE4 receptor in complex with APOE4 NTD
Citation | Zhou, J., Wang, Y., Huang, G., Yang, M., Zhu, Y., Jin, C., Jing,
D., Ji, K., Shi, Y. (2023). LilrB3 is a putative cell surface receptor of
APOE4. Cell Res., 33, 116-130. PMID: 36588123. DOI: 10.1038/s41422-022-00759-y
Gene source | Homo sapiens (human)
CryoEM Map | EMDB 34216 — open map
Experimental method | Electron microscopy
Resolution | 3.0Å
> open 34216 fromDatabase emdb
Summary of feedback from opening 34216 fetched from emdb
---
note | Fetching compressed map 34216 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-34216/map/emd_34216.map.gz
Opened emdb 34216 as #2, grid size 256,256,256, pixel 1.1, shown at level
0.196, step 1, values float32
> isolde start
> set selectionWidth 4
> isolde set simFidelityMode Highest/Slowest
ISOLDE: setting sim fidelity mode to Highest/Slowest
nonbonded_cutoff_distance = 1.700000
use_gbsa = True
gbsa_cutoff = 2.000000
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 138 residues in model #1 to IUPAC-IUB
standards.
8grx title:
APOE4 receptor in complex with APOE4 NTD [more info...]
Chain information for 8grx
---
Chain | Description | UniProt
1.2/A 1.2/C | Apolipoprotein E | APOE_HUMAN 23-162
1.2/B 1.2/D | Leukocyte immunoglobulin-like receptor subfamily A member 6 |
LIRA6_HUMAN 25-420
> clipper associate #2 toModel #1
Opened emdb 34216 as #1.1.1.1, grid size 256,256,256, pixel 1.1, shown at step
1, values float32
> addh
Summary of feedback from adding hydrogens to 8grx #1.2
---
warnings | Not adding hydrogens to /B PRO 66 N because it is missing heavy-
atom bond partners
Not adding hydrogens to /B PRO 66 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /B GLU 67 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /B PRO 68 N because it is missing heavy-atom bond
partners
Not adding hydrogens to /B PRO 68 CB because it is missing heavy-atom bond
partners
11 messages similar to the above omitted
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /B PRO 66 N; /D PRO 68 N; /D PRO 66 N; /B PRO 68 N
notes | Termini for 8grx (#1.2) chain A determined from SEQRES records
Termini for 8grx (#1.2) chain B determined from SEQRES records
Termini for 8grx (#1.2) chain C determined from SEQRES records
Termini for 8grx (#1.2) chain D determined from SEQRES records
Chain-initial residues that are actual N termini: /A GLY 23, /B PRO 25, /C GLY
23, /D PRO 25
Chain-initial residues that are not actual N termini: /A ALA 86, /B LYS 78, /C
ALA 86, /D LYS 78
Chain-final residues that are actual C termini: /A TYR 162, /B GLY 420, /C TYR
162, /D GLY 420
Chain-final residues that are not actual C termini: /A THR 83, /B ARG 71, /C
THR 83, /D ARG 71
Missing OXT added to C-terminal residue /A TYR 162
Missing OXT added to C-terminal residue /B GLY 420
Missing OXT added to C-terminal residue /C TYR 162
Missing OXT added to C-terminal residue /D GLY 420
884 hydrogen bonds
Adding 'H' to /A ALA 86
Adding 'H' to /B LYS 78
Adding 'H' to /C ALA 86
Adding 'H' to /D LYS 78
8054 hydrogens added
> ui tool show "Ramachandran Plot"
> isolde sim start /B:331
ISOLDE: started sim
> isolde cisflip /B:331
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /D:331
ISOLDE: started sim
> isolde cisflip /D:331
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:229
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1
16386 atoms, 16616 bonds, 4 pseudobonds, 1056 residues, 22 models selected
> isolde sim start /A-D
Sim termination reason: None
ISOLDE: stopped sim
> ui tool show Shell
0.00s - Debugger warning: It seems that frozen modules are being used, which
may
0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off
0.00s - to python to disable frozen modules.
0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to
disable this validation.
> swapaa mousemode sel GLU
> swapaa mousemode sel LEU
> swapaa mousemode sel ASP
> swapaa mousemode sel ARG
> select up
24 atoms, 23 bonds, 1 residue, 1 model selected
> swapaa mousemode sel GLU
> swapaa mousemode sel LEU
> swapaa mousemode sel ASP
> swapaa mousemode sel ARG
> volume gaussian #1 bfactor 80
Opened emdb 34216 gaussian as #2, grid size 256,256,256, pixel 1.1, shown at
step 1, values float32
> clipper associate #2 toModel #1
Opened emdb 34216 gaussian as #1.1.1.2, grid size 256,256,256, pixel 1.1,
shown at step 1, values float32
> cs 0.25
> alphafold match #1 trim false
Fetching compressed AlphaFold P02649 from
https://alphafold.ebi.ac.uk/files/AF-P02649-F1-model_v4.cif
Fetching compressed AlphaFold Q6PI73 from
https://alphafold.ebi.ac.uk/files/AF-Q6PI73-F1-model_v4.cif
2 AlphaFold models found using UniProt identifiers: P02649 (chains A,C),
Q6PI73 (chains B,D)
AlphaFold prediction matching 8grx
---
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id
A C | P02649 | APOE_HUMAN | 1.09 | 317 | 138 | 99
B D | Q6PI73 | LIRA6_HUMAN | 2.54 | 481 | 390 | 98
Opened 4 AlphaFold models
> matchmaker #2.2 to #1.2
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 8grx, chain B (#1.2) with AlphaFold LIRA6_HUMAN chain B, chain B
(#2.2), sequence alignment score = 1908.7
RMSD between 271 pruned atom pairs is 0.906 angstroms; (across all 390 pairs:
2.538)
> color #2.2 bychain
> color #2.2 byhetero
> color modify #2.2 hue + 50
ISOLDE: attempting to load PAE matrix for model #2.2 from the AlphaFold-EBI
database. If this fails or you wish to use a different PAE matrix, use the
"Load PAE matrix" button in ISOLDE's reference model restraints widget.
> alphafold pae #2.2 uniprotId Q6PI73 plot false
Fetching compressed AlphaFold PAE Q6PI73 from
https://alphafold.ebi.ac.uk/files/AF-Q6PI73-F1-predicted_aligned_error_v4.json
s1:
.............................................................................................................................................................................................................................................GQRWELALGRFWDYLRWVQT.......LSEQVQEELLS.SQVTQELRALMDETMKELKAYKSELEEQLTPVAEETRARLSKELQAAQARLGADMEDVRGRLVQYRGEVQAMLGQS.....TEELRVRLASHLRKLRKRLLRDADDLQKRLAVY.................................................................................................
s2:
MTPALTALLCLGLSLGPRTRVQAGPFPKPTLWAEPGSVISWGSPVTIWCQGSLEAQEYQLDKEGSPEPLDRNNPLEPKNKARFSIPSMTQHHAGRYRCHYYSSAGWSEPSDPLELVMTGFYNKPTLSALPSPVVASGGNMTLRCGSQKGYHHFVLMKEGEHQLPRTLDSQQLHSGGFQALFPVGPVTPSHRWRFTCYYYYTNTPRVWSHPSDPLEILPSGVSRKPSLLTLQGPVLAPGQSLTLQCGSDVGYDRFVLYKEGERDFLQRPGQQPQAGLSQANFTLGPVSPSHGGQYRCYGAH...NLSSEWSAPSDPLNI.LMAGQIYDTVSLSAQPGPTVA.SGENVTLLCQSRGYFDTFLLTKEGAAH.PPLRLRSMYGAHKYQAEFPMSPVTSAHAGTYRCYGSYSSNPHLLSFPSEPLELMVSGHSGGSSLPPTGPPSTPASHAKDYTVENLIRMGMAGLVLVFLGILLFEAQHSQRNPQDAAGR
s1:
........................PFPKPTLWAEPGSVISWGSPVTIWCQGSLEAQEYRLDKEGSPEPLDRNNPLEPKNKARFSIPSMTEHHAGRYRCHYYSSAGWSEPSDPLELVMTGFYNKPTLSALPSPVVASGGNMTLRCGSQKGYHHFVLMKEGEHQLPRTLDSQQLHSGGFQALFPVGPVNPSHRWRFTCYYYYMNTPQVWSHPSDPLEILPSGVSRKPSLLTLQGPVLAPGQSLTLQCGSDVGYDRFVLYKEGERDFLQRPGQQPQAGLSQANFTLGPVSRSHGGQYRCYGAHNLSSEWSAPSDPLNILMAGQIYDTVSLSAQPGPTVASGENVTLLCQSWWQFDTFLLTKEGAAHPPLRLRSMYGAHKYQAEFPMSPVTSAHAGTYRCYGSYSSNPHLLSFPSEPLELMVSG.............................................................
s2:
MTPALTALLCLGLSLGPRTRVQAGPFPKPTLWAEPGSVISWGSPVTIWCQGSLEAQEYQLDKEGSPEPLDRNNPLEPKNKARFSIPSMTQHHAGRYRCHYYSSAGWSEPSDPLELVMTGFYNKPTLSALPSPVVASGGNMTLRCGSQKGYHHFVLMKEGEHQLPRTLDSQQLHSGGFQALFPVGPVTPSHRWRFTCYYYYTNTPRVWSHPSDPLEILPSGVSRKPSLLTLQGPVLAPGQSLTLQCGSDVGYDRFVLYKEGERDFLQRPGQQPQAGLSQANFTLGPVSPSHGGQYRCYGAHNLSSEWSAPSDPLNILMAGQIYDTVSLSAQPGPTVASGENVTLLCQSRGYFDTFLLTKEGAAHPPLRLRSMYGAHKYQAEFPMSPVTSAHAGTYRCYGSYSSNPHLLSFPSEPLELMVSGHSGGSSLPPTGPPSTPASHAKDYTVENLIRMGMAGLVLVFLGILLFEAQHSQRNPQDAAGR
s1:
.............................................................................................................................................................................................................................................GQRWELALGRFWDYLRWVQT.......LSEQVQEELLS.SQVTQELRALMDETMKELKAYKSELEEQLTPVAEETRARLSKELQAAQARLGADMEDVRGRLVQYRGEVQAMLGQS.....TEELRVRLASHLRKLRKRLLRDADDLQKRLAVY.................................................................................................
s2:
MTPALTALLCLGLSLGPRTRVQAGPFPKPTLWAEPGSVISWGSPVTIWCQGSLEAQEYQLDKEGSPEPLDRNNPLEPKNKARFSIPSMTQHHAGRYRCHYYSSAGWSEPSDPLELVMTGFYNKPTLSALPSPVVASGGNMTLRCGSQKGYHHFVLMKEGEHQLPRTLDSQQLHSGGFQALFPVGPVTPSHRWRFTCYYYYTNTPRVWSHPSDPLEILPSGVSRKPSLLTLQGPVLAPGQSLTLQCGSDVGYDRFVLYKEGERDFLQRPGQQPQAGLSQANFTLGPVSPSHGGQYRCYGAH...NLSSEWSAPSDPLNI.LMAGQIYDTVSLSAQPGPTVA.SGENVTLLCQSRGYFDTFLLTKEGAAH.PPLRLRSMYGAHKYQAEFPMSPVTSAHAGTYRCYGSYSSNPHLLSFPSEPLELMVSGHSGGSSLPPTGPPSTPASHAKDYTVENLIRMGMAGLVLVFLGILLFEAQHSQRNPQDAAGR
s1:
........................PFPKPTLWAEPGSVISWGSPVTIWCQGSLEAQEYRLDKEGSPEPLDRNNPLEPKNKARFSIPSMTEHHAGRYRCHYYSSAGWSEPSDPLELVMTGFYNKPTLSALPSPVVASGGNMTLRCGSQKGYHHFVLMKEGEHQLPRTLDSQQLHSGGFQALFPVGPVNPSHRWRFTCYYYYMNTPQVWSHPSDPLEILPSGVSRKPSLLTLQGPVLAPGQSLTLQCGSDVGYDRFVLYKEGERDFLQRPGQQPQAGLSQANFTLGPVSRSHGGQYRCYGAHNLSSEWSAPSDPLNILMAGQIYDTVSLSAQPGPTVASGENVTLLCQSWWQFDTFLLTKEGAAHPPLRLRSMYGAHKYQAEFPMSPVTSAHAGTYRCYGSYSSNPHLLSFPSEPLELMVSG.............................................................
s2:
MTPALTALLCLGLSLGPRTRVQAGPFPKPTLWAEPGSVISWGSPVTIWCQGSLEAQEYQLDKEGSPEPLDRNNPLEPKNKARFSIPSMTQHHAGRYRCHYYSSAGWSEPSDPLELVMTGFYNKPTLSALPSPVVASGGNMTLRCGSQKGYHHFVLMKEGEHQLPRTLDSQQLHSGGFQALFPVGPVTPSHRWRFTCYYYYTNTPRVWSHPSDPLEILPSGVSRKPSLLTLQGPVLAPGQSLTLQCGSDVGYDRFVLYKEGERDFLQRPGQQPQAGLSQANFTLGPVSPSHGGQYRCYGAHNLSSEWSAPSDPLNILMAGQIYDTVSLSAQPGPTVASGENVTLLCQSRGYFDTFLLTKEGAAHPPLRLRSMYGAHKYQAEFPMSPVTSAHAGTYRCYGSYSSNPHLLSFPSEPLELMVSGHSGGSSLPPTGPPSTPASHAKDYTVENLIRMGMAGLVLVFLGILLFEAQHSQRNPQDAAGR
> sequence chain #1/B
Alignment identifier is 1.2/B
> sequence chain #2/B
Alignment identifier is 2.2/B
> isolde restrain distances "#1.2/B" templateAtoms "#2.2/B" perChain false
> adjustForConfidence true useCoordinateAlignment false kappa 4.40 fallOff
> 2.50 groupName "Reference Distance Restraints"
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]ISOLDE: Corrected atom nomenclature of 66 residues in
model #2.2 to IUPAC-IUB standards.
> isolde restrain torsions #1.2/B templateResidues #2.2/B adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain distances "#1.2/D" templateAtoms "#2.2/B" perChain false
> adjustForConfidence true useCoordinateAlignment false kappa 4.40 fallOff
> 2.50 groupName "Reference Distance Restraints"
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain torsions #1.2/D templateResidues #2.2/B adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> ui tool show "Model Panel"
> hide #!2 models
> select #1
16502 atoms, 16736 bonds, 4 pseudobonds, 1056 residues, 25 models selected
> isolde sim start #1.2/A-D
ISOLDE: started sim
> isolde sim pause
> show #!2 models
> show #2/D
> color byhetero
> select up
21 atoms, 21 bonds, 1 residue, 1 model selected
> select up
95 atoms, 96 bonds, 6 residues, 2 models selected
> ra
> isolde sim resume
> isolde sim pause
> select up
20 atoms, 20 bonds, 1 residue, 1 model selected
> select up
98 atoms, 99 bonds, 7 residues, 2 models selected
> ra
> select up
11 atoms, 10 bonds, 1 residue, 2 models selected
> select up
59 atoms, 58 bonds, 4 residues, 2 models selected
> ra
> isolde sim resume
> isolde sim pause
> hide #!2 models
> isolde sim resume
> select up
17 atoms, 17 bonds, 1 residue, 1 model selected
> ra
> select #1
16502 atoms, 16736 bonds, 4 pseudobonds, 1056 residues, 25 models selected
> ra
> isolde sim pause
> st first
> select clear
> st
[Repeated 14 time(s)]
> isolde sim resume
> st
[Repeated 18 time(s)]
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 19 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> awsf
> isolde sim start #1.2/A:51,57,119,1000
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> st
[Repeated 3 time(s)]
> isolde sim start #1.2/A:61,112
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 10 time(s)]
> isolde sim start #1.2/A:72
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> st
[Repeated 4 time(s)]
> isolde sim start #1.2/A:76
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 2 time(s)]
> isolde sim start #1.2/A:80
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 11 time(s)]
> isolde sim start #1.2/A:94
ISOLDE: started sim
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> st
[Repeated 1 time(s)]
> isolde sim start #1.2/A:96
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 1 time(s)]
> isolde sim start #!1.2/A:98
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 4 time(s)]
> isolde sim start #1.2/A:103
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 4 time(s)]
> isolde sim start #1.2/A:108
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
> sequence chain #1/A
Alignment identifier is 1.2/A
> ui mousemode right "mark point"
> marker #3 position 116.2,155.3,137.1 color yellow radius 1
> Label sel text "R112 (E4), C112 (E2/3) "
Unknown command: Label sel text "R112 (E4), C112 (E2/3) "
> label sel text "R112 (E4), C112 (E2/3) "
> select clear
> view #1/A:158
> ~label
> select #3
1 atom, 1 residue, 1 model selected
> label sel text "R112 (E4), C112 (E2/3) "
> hide #!3 models
> save R112_model.cif #1
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 103, in provider_save
remember_file(session, path, data_format.nicknames[0],
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/filehistory.py", line 230, in remember_file
h.remember_file(filename, format, models, database = database, file_saved =
file_saved,
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/filehistory.py", line 68, in remember_file
self.capture_thumbnails_cb()
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/filehistory.py", line 82, in capture_thumbnails_cb
if models != 'all models':
^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/orderedset.py", line 73, in __ne__
if isinstance(other, collections.Set):
^^^^^^^^^^^^^^^
AttributeError: module 'collections' has no attribute 'Set'
AttributeError: module 'collections' has no attribute 'Set'
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/orderedset.py", line 73, in __ne__
if isinstance(other, collections.Set):
^^^^^^^^^^^^^^^
See log for complete Python traceback.
> ui tool show Shell
OpenGL version: 3.3.0 NVIDIA 515.105.01
OpenGL renderer: NVIDIA GeForce RTX 3070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.2
Locale: en_GB.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: Dell Inc.
Model: XPS 8950
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 20 12th Gen Intel(R) Core(TM) i7-12700
Cache Size: 25600 KB
Memory:
total used free shared buff/cache available
Mem: 31Gi 12Gi 2.7Gi 513Mi 16Gi 18Gi
Swap: 2.0Gi 1.2Gi 862Mi
Graphics:
0000:01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA104 [GeForce RTX 3070 Lite Hash Rate] [10de:2488] (rev a1)
Subsystem: Dell GA104 [GeForce RTX 3070 Lite Hash Rate] [1028:c903]
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
blosc2: 2.0.0
build: 0.10.0
certifi: 2023.5.7
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.11
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: 1.45.7
ChimeraX-AtomicLibrary: 10.0.7
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: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.3
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-Clipper: 0.22.0
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: 1.7.dev202306142048
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: 1.1.2
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-ISOLDE: 1.7.dev0
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.2
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: 2.1
ChimeraX-MCopy: 1.0
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: 1.10.2
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0.1
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: 1.2
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: 2.1.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12
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: 1.2.2
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.29.1
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2.1
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: 1.1.0
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
distro: 1.7.0
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.40.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2023.3.16
imagesize: 1.4.1
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.1
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
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: 3.5.3
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.6
PyOpenGL-accelerate: 3.1.6
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: 25.1.0
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.31.0
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: 3.8.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.2
traitlets: 5.9.0
typing-extensions: 4.6.3
tzdata: 2023.3
urllib3: 2.0.3
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
Change History (3)
comment:2 by , 2 years ago
| Component: | Unassigned → Core |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → "Set" no longer directly in collections module |
comment:3 by , 2 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
Note:
See TracTickets
for help on using tickets.
