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Opened 2 years ago
Last modified 2 years ago
#9310 assigned defect
Chain type wrong when edited structure reopened
| Reported by: | Tristan Croll | Owned by: | Greg Couch |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | Eric Pettersen | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
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
I saved the attached mmCIF after doing some rebuilding work on 8grx (including mutating residues 112 and 158 of chain A from CYS to ARG using "swapaa mousemode sel ARG" for each, adding a couple of water molecules, and adding N-linked sugars to chain B). On re-opening chain A is being identified as PT_NONE rather than PT_AMINO.
Just checked what happens after I make the same changes to chains C and D, and sure enough chain C (equivalent to A) is also registered as PT_NONE on reopening. I'm guessing it's because the sequence changes aren't being properly passed into the saved mmCIF?
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
> open /home/tcroll/structure_dump/apoe4/8grx_apoe4_lilrb3/R112_model.cif
Chain information for R112_model.cif #4
---
Chain | Description
A C | Apolipoprotein E
B D | Leukocyte immunoglobulin-like receptor subfamily A member 6
> open 34216 fromDatabase emdb
Opened emdb 34216 as #5, grid size 256,256,256, pixel 1.1, shown at level
0.196, step 1, values float32
> hide #!1 models
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #4 to IUPAC-IUB
standards.
Chain information for R112_model.cif
---
Chain | Description
4.2/A 4.2/C | Apolipoprotein E
4.2/B 4.2/D | Leukocyte immunoglobulin-like receptor subfamily A member 6
> clipper associate #5 toModel #4
Opened emdb 34216 as #4.1.1.1, grid size 256,256,256, pixel 1.1, shown at step
1, values float32
> swapaa mousemode sel CYS
> isolde sim start #4.2/A:61,112
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> show #!1 models
> hide #!4 models
3 models selected
> select clear
> show #!3 models
> ui mousemode right "resize markers"
> marker change #3:1 radius 0.5916
> select up
24 atoms, 23 bonds, 1 residue, 1 model selected
> color sel brown
> color byhetero
> color sel orange
> color byhetero
> select #4/A:112
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel orange
> color byhetero
> color #3 yellow
> select clear
> cofr showPivot false
> clipper isolate #1
> clipper isolate #4
> open 8grx
8grx title:
APOE4 receptor in complex with APOE4 NTD [more info...]
Chain information for 8grx #5
---
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
> surface #5
> color #5 byidentity
> label #5 surfaces text "{0.chain_id} "
Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword
> hide #!5 models
> view name detail
> show #!5 models
> select clear
> hide #!1 models
> hide #!3 models
> label #5/A,C:87 text "APOE "
> show #5/A,C:87@CA,CB
> label #5/A,C:87 text "APOE " height 4
> label #5/B,D:54 text "LILRA6 " height 4
> select clear
> movie record
> movie stop
> movie record size 1920,1080
> rock y 60 120 cycle 120
> view detail frames 60
> movie crossfade 30
> hide #5 models
> show #!1 models
> show #3 models
> rock y 40 120 cycle 120
> movie crossfade 60
> hide #!1 models
> show #!4 models
> rock y 40 120 cycle 120
> movie stop
> movie encode 8grx_error.mp4
Movie saved to 8grx_error.mp4
> view #1/A:158
> view #1/C:158
> view #1/A:158
> select clear
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 66 residues in model #2.4 to IUPAC-IUB
standards.
ISOLDE: created disulfide bonds between the following residues:
D49-D98; D245-D296; D144-D196; D345-D396
> select up
24 atoms, 23 bonds, 1 residue, 1 model selected
> color sel orange target a
> color sel byhetero
> select up
24 atoms, 23 bonds, 1 residue, 1 model selected
> swapaa mousemode sel CYS
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel orange target a
> color sel byhetero
> isolde sim start #4.2/A:96,103,154,158
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 #4.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> show #!1 models
> color #1/A:158 orange
> color #1 byhetero
> select clear
> ui mousemode right "mark point"
> marker #3 position 103.2,147.2,154.4 color yellow radius 0.5916
> label sel text "R158 (E3/4) / C158 (E2) "
> hide #!4 models
> select clear
> clipper isolate #1
> clipper isolate #4
> hide #!1 models
> show #!4 models
> hide #!4 models
> show #!1 models
> cofr showPivot false
> movie record size 1920,1080
> rock y 40 120 cycle 120
> movie crossfade 30
> hide #!1 models
> show #!4 models
> rock y 40 120 cycle 120
> movie stop
> movie encode 8grx_158.mp4
Movie saved to 8grx_158.mp4
> clipper spotlight
> isolde sim start #!4.2/A:156
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 first
> st
[Repeated 14 time(s)]
> select clear
> st
[Repeated 40 time(s)]
> close #1
> volume gaussian #4 bfactor 80
Opened emdb 34216 gaussian as #1, grid size 256,256,256, pixel 1.1, shown at
step 1, values float32
> clipper associate #1 toModel #4
Opened emdb 34216 gaussian as #4.1.1.2, grid size 256,256,256, pixel 1.1,
shown at step 1, values float32
> st
[Repeated 16 time(s)]
> ui tool show Shell
> color brown
> color byhetero
> cbc
> color #1 cyan target s
> color #1 cyan target v
Invalid "target" argument: Character 'v' is not an allowed target, must be one
of acrsbmpfl
> color #1 cyan target m
> color #4 cyan target m
> cbc
> st
[Repeated 15 time(s)]
> aw
> isolde sim start #4.2/A:114,1001
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> open 8grx
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
> show #1
> hide #!1 models
> st
[Repeated 10 time(s)]
> isolde sim start #4.2/A:125,128
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 #4.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> st
[Repeated 8 time(s)]
> isolde sim start #4.2/A:134
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 5 time(s)]
> show #!1 models
> hide #!1 models
> isolde sim start #4.2/A:140
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 8 time(s)]
> isolde sim start #4.2/A:149
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 29 time(s)]
> isolde sim start #!4.2/B:41
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
> isolde pepflip #4.2/B:121
ISOLDE: started sim
> isolde pepflip #4.2/B:121
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 18 time(s)]
> isolde sim start #4.2/B:59-60,99
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 2 time(s)]
> select up
167 atoms, 167 bonds, 11 residues, 2 models selected
> isolde sim start #4.2/B:63-79
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 #4.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> st
[Repeated 25 time(s)]
> isolde sim start #4.2/B:95
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 19 time(s)]
> isolde sim start #4.2/B:115,205
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 #4.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> st
[Repeated 18 time(s)]
> isolde sim start #4.2/B:134
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)]
> al NAG
Deleted the following atoms from residue NAG B1000: HO1, O1
> show sel
> ui mousemode right "translate selected atoms"
> delete sel
> isolde sim start #4.2/B:139,1000
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 #4.2/B:141
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)]
> select up
31 atoms, 30 bonds, 2 residues, 2 models selected
> select up
253 atoms, 256 bonds, 15 residues, 2 models selected
> select up
265 atoms, 267 bonds, 16 residues, 2 models selected
> select up
312 atoms, 315 bonds, 19 residues, 2 models selected
> isolde sim start #4.2/B:152-170
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
> ht NE
Set protonation of HIS #4.2/B:152 to NE
> select up
36 atoms, 35 bonds, 2 residues, 2 models selected
> select up
185 atoms, 185 bonds, 11 residues, 2 models selected
> select up
199 atoms, 199 bonds, 12 residues, 2 models selected
> select up
312 atoms, 315 bonds, 19 residues, 2 models selected
> isolde sim start #4.2/B:152-170
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 3 time(s)]
> select up
17 atoms, 16 bonds, 1 residue, 2 models selected
> select up
127 atoms, 128 bonds, 8 residues, 2 models selected
> isolde sim start #4.2/B:159-166
ISOLDE: started sim
> select clear
> isolde pepflip #4.2/B:160
[Repeated 1 time(s)]
> isolde pepflip #4.2/B:163
> isolde pepflip #4.2/B:162
[Repeated 1 time(s)]
> isolde pepflip #4.2/B:161
> isolde pepflip #4.2/B:162
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 23 time(s)]
> isolde sim start #4.2/B:180
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 8 time(s)]
> isolde sim start #4.2/B:190
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
> ht ND
Set protonation of HIS #4.2/B:190 to ND
> isolde sim start #4.2/B:189-190
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 1 time(s)]
> isolde sim start #4.2/B:191
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 3 time(s)]
> isolde sim start #4.2/B:195
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 13 time(s)]
> ht ND
Set protonation of HIS #4.2/B:209 to ND
> isolde sim start #4.2/B:209
ISOLDE: started sim
> select clear
> isolde sim resume
> 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 #4.2/B:214
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 18 time(s)]
> aw
> isolde sim start #4.2/B:233,1001
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 6 time(s)]
> isolde sim start #4.2/B:240
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 3 time(s)]
> isolde sim start #4.2/B:244
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> al NAG
Deleted the following atoms from residue NAG B1002: O1, HO1
> show sel
> ui mousemode right "translate selected atoms"
> delete sel
> isolde sim start #4.2/B:280,1002
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
> isolde sim start #4.2/B:245
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 3 time(s)]
> isolde sim start #4.2/B:249
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 3 time(s)]
> isolde sim start #4.2/B:253
ISOLDE: started sim
> isolde sim resume
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 5 time(s)]
> isolde sim start #4.2/B:259
ISOLDE: started sim
> isolde pepflip #4.2/B:260
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #4.2/B:259,293,295
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 #4.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> st
[Repeated 2 time(s)]
> isolde sim start #4.2/B:262
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 #4.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> st
[Repeated 3 time(s)]
> isolde sim start #4.2/B:266
ISOLDE: started sim
> select clear
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 28 time(s)]
> isolde sim start #4.2/B:295
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 6 time(s)]
> al NAG
Deleted the following atoms from residue NAG B1003: HO1, O1
> show sel
> ui mousemode right "translate selected atoms"
> delete sel
> isolde sim start #4.2/B:301,1003
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 7 time(s)]
> isolde sim start #4.2/B:310
ISOLDE: started sim
> isolde pepflip #4.2/B:311
[Repeated 1 time(s)]
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 3 time(s)]
> isolde sim start #4.2/B:405
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 11 time(s)]
> isolde sim start #4.2/B:325
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 13 time(s)]
> al NAG
Deleted the following atoms from residue NAG B1004: HO1, O1
> show sel
> ui mousemode right "translate selected atoms"
> delete sel
> isolde sim start #4.2/B:340,1004
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 #4.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> st
[Repeated 1 time(s)]
> isolde sim start #4.2/B:342,380
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 3 time(s)]
> isolde sim start #4.2/B:346
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 1 time(s)]
> isolde sim start #4.2/B:348
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 #4.2/B:353
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 3 time(s)]
> isolde sim start #4.2/B:357
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 5 time(s)]
> isolde sim start #4.2/B:363
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 5 time(s)]
> isolde sim start #4.2/B:369
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 #4.2/B:371
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 #4.2/B:373
ISOLDE: started sim
> isolde pepflip #4.2/B:374
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 25 time(s)]
> isolde sim start #4.2/B:399
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 #4.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> st
[Repeated 12 time(s)]
> isolde sim start #4.2/B:412
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 #4.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> st
[Repeated 8 time(s)]
> pwd
Current working directory is:
/home/tcroll/structure_dump/apoe4/8grx_apoe4_lilrb3
> save 8grx_apoe2_working.cif #4
Not saving entity_poly_seq for non-authoritative sequences
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.
> hide #!6 models
> close #6
> select :NAG
112 atoms, 112 bonds, 4 residues, 1 model selected
> clipper isolate sel
> clipper spotlight
> save working.cxs
Taking snapshot of stepper: R112_model.cif
> open 8grx_apoe2_working.cif
Summary of feedback from opening 8grx_apoe2_working.cif
---
warnings | Unknown polymer entity '1' near line 2632
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for 8grx_apoe2_working.cif #6
---
Chain | Description
B D | Leukocyte immunoglobulin-like receptor subfamily A member 6
C | Apolipoprotein E
> show #6
> close #6
> save 8grx_apoe2_working.pdb #4
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.
> open 8grx_apoe2_working.pdb
Chain information for 8grx_apoe2_working.pdb #6
---
Chain | Description
A | No description available
B D | No description available
C | No description available
> color #6 bychain
> matchmaker #6/A to #4/B
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 R112_model.cif, chain B (#4.2) with 8grx_apoe2_working.pdb, chain A
(#6), sequence alignment score = 5.4
Fewer than 3 residues aligned; cannot match R112_model.cif, chain B with
8grx_apoe2_working.pdb, chain A
> matchmaker #6/A to #4/C
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 R112_model.cif, chain C (#4.2) with 8grx_apoe2_working.pdb, chain A
(#6), sequence alignment score = 690.9
RMSD between 138 pruned atom pairs is 0.167 angstroms; (across all 138 pairs:
0.167)
> delete #4/C,D
> delete #6/C,D
> select #6
8342 atoms, 8460 bonds, 2 pseudobonds, 535 residues, 2 models selected
ISOLDE: merge models
Merging models #6 into #4.2.
Remapping chain ID A in #6 to C
Remapping chain ID B in #6 to D
> hide #!6 models
> show #4&~HC
> select #4
16684 atoms, 16920 bonds, 4 pseudobonds, 1070 residues, 25 models selected
> isolde sim start #4.2/A-D
ISOLDE: started sim
> select clear
> isolde sim pause
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #4.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> open
> /home/tcroll/structure_dump/apoe4/8grx_apoe4_lilrb3/8grx_apoe2_working.cif
Summary of feedback from opening
/home/tcroll/structure_dump/apoe4/8grx_apoe4_lilrb3/8grx_apoe2_working.cif
---
warnings | Unknown polymer entity '1' near line 2632
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for 8grx_apoe2_working.cif #7
---
Chain | Description
B D | Leukocyte immunoglobulin-like receptor subfamily A member 6
C | Apolipoprotein E
> show #7
> hide #7
> ui tool show Shell
> save test.cif #4
Not saving entity_poly_seq for non-authoritative sequences
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.
> open test.cif
Summary of feedback from opening test.cif
---
warnings | Unknown polymer entity '1' near line 2210
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for test.cif #8
---
Chain | Description
B D | Leukocyte immunoglobulin-like receptor subfamily A member 6
> hide #!7 models
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 11Gi 14Gi 464Mi 4.2Gi 18Gi
Swap: 2.0Gi 1.8Gi 190Mi
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
File attachment: 8grx_apoe2_working.cif
Attachments (1)
Change History (3)
by , 2 years ago
| Attachment: | 8grx_apoe2_working.cif added |
|---|
comment:1 by , 2 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Input/Output |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Chain type wrong when edited structure reopened |
comment:2 by , 2 years ago
| Description: | modified (diff) |
|---|
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