QMainWindowLayout::tabPosition called with out-of-bounds value '0'

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19044
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted

Thread 0x00006494 (most recent call first):
  File "D:\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 576 in _handle_results
  File "D:\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "D:\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00005964 (most recent call first):
  File "D:\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 528 in _handle_tasks
  File "D:\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "D:\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x000057a4 (most recent call first):
  File "D:\ChimeraX 1.3\bin\lib\multiprocessing\connection.py", line 816 in _exhaustive_wait
  File "D:\ChimeraX 1.3\bin\lib\multiprocessing\connection.py", line 884 in wait
  File "D:\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 499 in _wait_for_updates
  File "D:\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 519 in _handle_workers
  File "D:\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "D:\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x000061ec (most recent call first):
  File "D:\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "D:\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "D:\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00005d9c (most recent call first):
  File "D:\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "D:\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "D:\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Current thread 0x000055fc (most recent call first):
  File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:/Users/Léa/Downloads/Nt sequence RV1683.txt"

Unrecognized file suffix '.txt'  

> open C:/Users/Léa/Downloads/sequence.fasta

Summary of feedback from opening C:/Users/Léa/Downloads/sequence.fasta  
---  
note | Alignment identifier is sequence.fasta  
  
Opened 1 sequences from sequence.fasta  

> open C:\Users\Léa\Downloads\sequence.fasta format fasta

Summary of feedback from opening C:\Users\Léa\Downloads\sequence.fasta  
---  
notes | Destroying pre-existing alignment with identifier sequence.fasta  
Alignment identifier is sequence.fasta  
  
Opened 1 sequences from sequence.fasta  

> show atoms

> ui windowfill toggle

> show atoms

> hide atoms

> show cartoons

> hide cartoons

> style stick

Changed 0 atom styles  

> style sphere

Changed 0 atom styles  

> set bgColor white

> lighting simple

> lighting soft

> ui tool show "Selection Inspector"

> movie record

> turn y 2 180

> wait 180

> movie encode C:\Users\Léa\Desktop\movie1.mp4

Movie saved to \C:Users\\...\Desktop\movie1.mp4  
  

> style sphere

Changed 0 atom styles  

> style ball

Changed 0 atom styles  

> show atoms

> close #

Expected a models specifier or a keyword  

> view # clip false

Expected an objects specifier or a view name or a keyword  

> blastprotein sequence.fasta:1

ChimeraX REST job id: O33FG3L2HF3GDG9N  
BlastProtein finished.  
Parsing BLAST results.  

> lighting full

> select C

Nothing selected  

> ui mousemode right "mark maximum"

> undo

> open C:\Users\Léa\Downloads\sequence.fasta format fasta

Summary of feedback from opening C:\Users\Léa\Downloads\sequence.fasta  
---  
notes | Destroying pre-existing alignment with identifier sequence.fasta  
Alignment identifier is sequence.fasta  
  
Opened 1 sequences from sequence.fasta  

> open C:\Users\Léa\Downloads\sequence.fasta format fasta

Summary of feedback from opening C:\Users\Léa\Downloads\sequence.fasta  
---  
notes | Destroying pre-existing alignment with identifier sequence.fasta  
Alignment identifier is sequence.fasta  
  
Opened 1 sequences from sequence.fasta  

> open C:/Users/Léa/Downloads/sequence.fasta

Summary of feedback from opening C:/Users/Léa/Downloads/sequence.fasta  
---  
notes | Destroying pre-existing alignment with identifier sequence.fasta  
Alignment identifier is sequence.fasta  
  
Opened 1 sequences from sequence.fasta  

> ui mousemode right "mark surface"

> open C:/Users/Léa/Downloads/sequence.fasta

Summary of feedback from opening C:/Users/Léa/Downloads/sequence.fasta  
---  
notes | Destroying pre-existing alignment with identifier sequence.fasta  
Alignment identifier is sequence.fasta  
  
Opened 1 sequences from sequence.fasta  

> open C:/Users/Léa/Downloads/query.msa.fasta/query.msa.fasta

Summary of feedback from opening
C:/Users/Léa/Downloads/query.msa.fasta/query.msa.fasta  
---  
note | Alignment identifier is query.msa.fasta  
  
Traceback (most recent call last):  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py",
line 155, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\run.py",
line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2856, in run  
result = ci.function(session, **kw_args)  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2856, in run  
result = ci.function(session, **kw_args)  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 181, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 432, in collated_open  
return remember_data_format()  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 403, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\seqalign\\__init__.py",
line 61, in open  
return open_file(session, data, file_name,  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\seqalign\parse.py", line
56, in open_file  
alignments = [session.alignments.new_alignment(seqs,  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\seqalign\manager.py",
line 243, in new_alignment  
alignment = Alignment(self.session, seqs, identify_as, attrs, markups,
auto_destroy,  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\seqalign\alignment.py",
line 111, in __init__  
self._headers = [hdr_class(self) for hdr_class in
session.alignments.headers()]  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\seqalign\alignment.py",
line 111, in   
self._headers = [hdr_class(self) for hdr_class in
session.alignments.headers()]  
File "D:\ChimeraX 1.3\bin\lib\site-
packages\chimerax\alignment_headers\conservation.py", line 42, in __init__  
super().__init__(alignment, *args, eval_while_hidden=True, **kw)  
File "D:\ChimeraX 1.3\bin\lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 59, in __init__  
self.reevaluate()  
File "D:\ChimeraX 1.3\bin\lib\site-
packages\chimerax\alignment_headers\conservation.py", line 168, in reevaluate  
return super().reevaluate(pos1, pos2, evaluation_func=evaluation_func)  
File "D:\ChimeraX 1.3\bin\lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 206, in
reevaluate  
evaluation_func(pos1, pos2)  
File "D:\ChimeraX 1.3\bin\lib\site-
packages\chimerax\alignment_headers\conservation.py", line 274, in
_reeval_al2co  
result = subprocess.run(command, capture_output=True, text=True, check=True)  
File "D:\ChimeraX 1.3\bin\lib\subprocess.py", line 528, in run  
raise CalledProcessError(retcode, process.args,  
subprocess.CalledProcessError: Command '['D:\\\ChimeraX
1.3\\\bin\\\lib\\\site-
packages\\\chimerax\\\alignment_headers\\\bin\\\al2co.exe', '-i',
'C:\\\Users\\\LAB9CF~1\\\AppData\\\Local\\\Temp\\\tmphm4dk31i.aln', '-f', '2',
'-c', '0', '-w', '1', '-g', '0.5']' returned non-zero exit status 3221225786.  
  
subprocess.CalledProcessError: Command '['D:\\\ChimeraX
1.3\\\bin\\\lib\\\site-
packages\\\chimerax\\\alignment_headers\\\bin\\\al2co.exe', '-i',
'C:\\\Users\\\LAB9CF~1\\\AppData\\\Local\\\Temp\\\tmphm4dk31i.aln', '-f', '2',
'-c', '0', '-w', '1', '-g', '0.5']' returned non-zero exit status 3221225786.  
  
File "D:\ChimeraX 1.3\bin\lib\subprocess.py", line 528, in run  
raise CalledProcessError(retcode, process.args,  
  
See log for complete Python traceback.  
  

> open C:/Users/Léa/Downloads/sequence.fasta

Summary of feedback from opening C:/Users/Léa/Downloads/sequence.fasta  
---  
notes | Destroying pre-existing alignment with identifier sequence.fasta  
Alignment identifier is sequence.fasta  
  
Opened 1 sequences from sequence.fasta  

> show atoms

> set bgColor black

> show cartoons

> ui tool show "Selection Inspector"

> ui mousemode right "mark maximum"

> ui mousemode right "mark plane"

> ui mousemode right "mark maximum"

> ui mousemode right "mark plane"

> ui mousemode right "mark surface"

> ui mousemode right "mark center"

> ui mousemode right "resize markers"

> ui mousemode right select

> ui mousemode right rotate

> ui mousemode right translate

> ui mousemode right zoom

> ui mousemode right "translate selected models"

> select sel @ select clear

> select

Nothing selected  

> select helix

Nothing selected  

> select sequence NC_000962.3:19

Nothing selected  

> select sequence NC_000962.3:19

Nothing selected  

> close session

> help help:quickstart

> select sequence NC_000962.3:19

Nothing selected  

> select sequence RV1683

Nothing selected  

> select sequence RV1683

Nothing selected  

> help help:user/findseq.html

> select clear

> open C:/Users/Léa/Downloads/sequence.fasta

Summary of feedback from opening C:/Users/Léa/Downloads/sequence.fasta  
---  
note | Alignment identifier is sequence.fasta  
  
Opened 1 sequences from sequence.fasta  

> select sequence RV1683

Nothing selected  

> SEL

Unknown command: SEL  

> SEL

Unknown command: SEL  

> select backbone

Nothing selected  

> open C:\Users\Léa\Downloads\sequence.fasta format fasta

Summary of feedback from opening C:\Users\Léa\Downloads\sequence.fasta  
---  
notes | Destroying pre-existing alignment with identifier sequence.fasta  
Alignment identifier is sequence.fasta  
  
Opened 1 sequences from sequence.fasta  

> open C:\Users\Léa\Downloads\sequence.fasta format fasta

Summary of feedback from opening C:\Users\Léa\Downloads\sequence.fasta  
---  
notes | Destroying pre-existing alignment with identifier sequence.fasta  
Alignment identifier is sequence.fasta  
  
Opened 1 sequences from sequence.fasta  
No visible models!  

> select

Nothing selected  

> select

Nothing selected  

> select ions

Nothing selected  

> ui windowfill toggle

> nucleotides fill

> style nucleic stick

Changed 0 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> nucleotides tube/slab shape ellipsoid

> show cartoons

> open C:/Users/Léa/Downloads/sequence.fasta

Summary of feedback from opening C:/Users/Léa/Downloads/sequence.fasta  
---  
notes | Destroying pre-existing alignment with identifier sequence.fasta  
Alignment identifier is sequence.fasta  
  
Opened 1 sequences from sequence.fasta  

> ui dockable false "Sequence Viewer"

> open C:/Users/Léa/Downloads/AF-O33185-F1-model_v2.pdb

AF-O33185-F1-model_v2.pdb title:  
Alphafold monomer V2.0 prediction for possible bifunctional enzyme long-chain
acyl-coa synthase and lipase (O33185) [more info...]  
  
Chain information for AF-O33185-F1-model_v2.pdb #1  
---  
Chain | Description | UniProt  
A | possible bifunctional enzyme long-chain acyl-coa synthase and lipase |
O33185_MYCTU  
  

> set bgColor white

> set bgColor black

> lighting simple

> lighting full

> show atoms

> hide atoms

> show atoms

> hide cartoons

> style sphere

Changed 7562 atom styles  

> style ball

Changed 7562 atom styles  

> show cartoons

> style ball

Changed 7562 atom styles  

> hide atoms

> ui tool show "Side View"

> view

> lighting flat

> set bgColor gray

> lighting flat

> lighting shadows true intensity 0.5

> set bgColor white

> set bgColor black

> lighting soft

> graphics silhouettes false

> select /A

7562 atoms, 7725 bonds, 999 residues, 1 model selected  

> ui mousemode right "mark center"

> color sel bynucleotide

> ui mousemode right "mark maximum"

> ui mousemode right "mark plane"

> ui mousemode right "link markers"

> ui mousemode right "mark maximum"

Drag select of 4 residues  
Drag select of 999 residues  

> color sel bynucleotide

Alignment identifier is 1/A  

> color sel byhetero

> color sel bypolymer

> rainbow sel

> color sel bynucleotide

> color sel bypolymer

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for AF-O33185-F1-model_v2.pdb_A SES surface #1.1: minimum,
-22.15, mean -1.96, maximum 12.09  
To also show corresponding color key, enter the above coulombic command and
add key true  

> mlp sel

Map values for surface "AF-O33185-F1-model_v2.pdb_A SES surface": minimum
-30.98, mean -4.953, maximum 23.11  
To also show corresponding color key, enter the above mlp command and add key
true  

> color bfactor sel

7562 atoms, 999 residues, 1 surfaces, atom bfactor range 29.7 to 98.5  

> hbonds sel reveal true

879 hydrogen bonds found  

> hide sel cartoons

> nucleotides sel fill

> style nucleic & sel stick

Changed 0 atom styles  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> select #1/A:1-37

277 atoms, 278 bonds, 23 pseudobonds, 37 residues, 2 models selected  

> select #1/A:1-109

836 atoms, 859 bonds, 74 pseudobonds, 109 residues, 2 models selected  

> select #1/A:184-220

283 atoms, 291 bonds, 24 pseudobonds, 37 residues, 2 models selected  

> select #1/A:184-220

283 atoms, 291 bonds, 24 pseudobonds, 37 residues, 2 models selected  

> select
> #1/A:6-29,81-84,92-98,117-119,122-140,150-162,185-187,190-205,212-222,224-237,241-257,264-276,279-282,294-296,314-321,338-341,345-363,389-396,403-440,450-460,476-493,509-521,534-541,550-558,578-582,589-591,594-596,632-645,663-676,688-697,709-712,737-746,863-865,876-885,919-927,955-959,984-991

2922 atoms, 2935 bonds, 292 pseudobonds, 385 residues, 2 models selected  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  
Drag select of AF-O33185-F1-model_v2.pdb_A SES surface, 848260 of 849114
triangles, 4219 atoms, 4086 bonds, 879 pseudobonds  
Drag select of AF-O33185-F1-model_v2.pdb_A SES surface, 4219 atoms, 4086
bonds, 879 pseudobonds  
Destroying pre-existing alignment with identifier 1/A  
Alignment identifier is 1/A  
Destroying pre-existing alignment with identifier 1/A  
Alignment identifier is 1/A  

> ui tool show "Side View"

> view orient

> lighting soft

> hide sel atoms

> hide sel cartoons

> color sel bynucleotide

> select #1/A:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:1-378

2905 atoms, 2977 bonds, 343 pseudobonds, 378 residues, 2 models selected  

> sequence associate #1/A 1/A

Disassociated AF-O33185-F1-model_v2.pdb chain A from chain A  
Associated AF-O33185-F1-model_v2.pdb chain A to chain A with 0 mismatches  

> select
> #1/A:6-29,81-84,92-98,117-119,122-140,150-162,185-187,190-205,212-222,224-237,241-257,264-276,279-282,294-296,314-321,338-341,345-363,389-396,403-440,450-460,476-493,509-521,534-541,550-558,578-582,589-591,594-596,632-645,663-676,688-697,709-712,737-746,863-865,876-885,919-927,955-959,984-991

2922 atoms, 2935 bonds, 292 pseudobonds, 385 residues, 2 models selected  

> sequence associate #1/A 1/A

Disassociated AF-O33185-F1-model_v2.pdb chain A from chain A  
Associated AF-O33185-F1-model_v2.pdb chain A to chain A with 0 mismatches  

> open C:/Users/Léa/Downloads/4zxj.pdb

Summary of feedback from opening C:/Users/Léa/Downloads/4zxj.pdb  
---  
warning | Entry 4ZXJ superseded by entry 5T3D  
  
4zxj.pdb title:  
Crystal structure of holo-ENTF A nonribosomal peptide synthetase In the
thioester-forming conformation [more info...]  
  
Chain information for 4zxj.pdb #3  
---  
Chain | Description | UniProt  
A | enterobactin synthase component F | ENTF_ECOLI  
  
Drag select of 157 atoms, 1042 residues, 141 bonds  

> open C:/Users/Léa/Downloads/4zxj.pdb

Summary of feedback from opening C:/Users/Léa/Downloads/4zxj.pdb  
---  
warning | Entry 4ZXJ superseded by entry 5T3D  
  
4zxj.pdb title:  
Crystal structure of holo-ENTF A nonribosomal peptide synthetase In the
thioester-forming conformation [more info...]  
  
Chain information for 4zxj.pdb #4  
---  
Chain | Description | UniProt  
A | enterobactin synthase component F | ENTF_ECOLI  
  

> select #1/A:1-378

2905 atoms, 2977 bonds, 343 pseudobonds, 378 residues, 2 models selected  

> select
> #1/A:6-29,81-84,92-98,117-119,122-140,150-162,185-187,190-205,212-222,224-237,241-257,264-276,279-282,294-296,314-321,338-341,345-363,389-396,403-440,450-460,476-493,509-521,534-541,550-558,578-582,589-591,594-596,632-645,663-676,688-697,709-712,737-746,863-865,876-885,919-927,955-959,984-991

2922 atoms, 2935 bonds, 292 pseudobonds, 385 residues, 2 models selected  

> ui tool show "Modeller Comparative"

> modeller comparative 1/A:1 numModels 5 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false

No Modeller license key provided. Get a license key by registering at the
Modeller web site.  

> sequence associate #3/A 1/A

Associated 4zxj.pdb chain A to chain A with 971 mismatches and/or gaps  

> sequence disassociate #3/A

Disassociated 4zxj.pdb chain A from chain A  

> nucleotides sel tube/slab shape muffler

Drag select of 314 atoms, 2084 residues, 282 bonds  
Drag select of 314 atoms, 2064 residues, 282 bonds  
Drag select of 314 atoms, 2084 residues, 282 bonds  
Alignment identifier is 1  

> sequence header 1 rmsd show

Chains used in RMSD evaluation for alignment 1: 4zxj.pdb #3/A, 4zxj.pdb #4/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  

> sequence header 1 rmsd hide

Hiding rmsd header for alignment 1  

> ui tool show "Model Loops"

> modeller refine 1:1:all-missing 1/A:1:all-missing numModels 5 fast false
> adjacentFlexible 1 protocol standard

Traceback (most recent call last):  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\modeller\tool.py", line
229, in launch_modeller  
run(self.session, ("modeller %s %s numModels %d fast %s " % (sub_cmd, "
".join(aln_seq_args),  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\run.py",
line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2877, in run  
result = ci.function(session, *args, optional=optional,  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 3417, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2856, in run  
result = ci.function(session, **kw_args)  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\modeller\cmd.py", line
121, in model_loops  
loops.model(session, targets, adjacent_flexible=adjacent_flexible,
block=block, chains=chains,  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\modeller\loops.py", line
135, in model  
mmap = seq.match_maps[chain]  
KeyError:   
  
KeyError:  
  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\modeller\loops.py", line
135, in model  
mmap = seq.match_maps[chain]  
  
See log for complete Python traceback.  
  

> modeller refine 1:1:all-missing 1/A:1:all-missing numModels 5 fast false
> adjacentFlexible 1 protocol standard

Traceback (most recent call last):  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\modeller\tool.py", line
229, in launch_modeller  
run(self.session, ("modeller %s %s numModels %d fast %s " % (sub_cmd, "
".join(aln_seq_args),  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\run.py",
line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2877, in run  
result = ci.function(session, *args, optional=optional,  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 3417, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2856, in run  
result = ci.function(session, **kw_args)  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\modeller\cmd.py", line
121, in model_loops  
loops.model(session, targets, adjacent_flexible=adjacent_flexible,
block=block, chains=chains,  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\modeller\loops.py", line
135, in model  
mmap = seq.match_maps[chain]  
KeyError:   
  
KeyError:  
  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\modeller\loops.py", line
135, in model  
mmap = seq.match_maps[chain]  
  
See log for complete Python traceback.  
  

> modeller refine 1/A:1:all-missing numModels 5 fast false adjacentFlexible 1
> protocol standard

No Modeller license key provided. Get a license key by registering at the
Modeller web site.  

> hide sel surfaces

Drag select of AF-O33185-F1-model_v2.pdb_A SES surface  
Drag select of AF-O33185-F1-model_v2.pdb_A SES surface, 849095 of 849114
triangles  

> rainbow

> color bychain

> color bypolymer

> color bynucleotide

> hide surfaces

> show cartoons

> rainbow

> mlp

Map values for surface "AF-O33185-F1-model_v2.pdb_A SES surface": minimum
-30.98, mean -4.953, maximum 23.11  
Map values for surface "4zxj.pdb_A SES surface": minimum -32.74, mean -4.762,
maximum 24.22  
To also show corresponding color key, enter the above mlp command and add key
true  

> select
> #3/A:10-21,40-58,95-105,110-114,145-162,173-204,234-244,248-265,281-286,305-323,327-335,402-423,437-446,456-468,483-500,515-529,540-552,617-631,649-661,670-686,693-703,705-713,727-739,761-767,816-823,869-878,893-897,918-935,954-958,975-989,1005-1020,1025-1032,1034-1044
> #4/A:10-21,40-58,95-105,110-114,145-162,173-204,234-244,248-265,281-286,305-323,327-335,402-423,437-446,456-468,483-500,515-529,540-552,617-631,649-661,670-686,693-703,705-713,727-739,761-767,816-823,869-878,893-897,918-935,954-958,975-989,1005-1020,1025-1032,1034-1044

6542 atoms, 6600 bonds, 864 residues, 2 models selected  

> hbonds sel reveal true

2076 hydrogen bonds found  

> select #1/A:1-378

2905 atoms, 2977 bonds, 378 residues, 1 model selected  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> color sel bynucleotide

Drag select of AF-O33185-F1-model_v2.pdb_A SES surface, 4zxj.pdb_A SES
surface, 2121 of 827218 triangles, 4zxj.pdb_A SES surface, 2121 of 827218
triangles, 999 residues  
Drag select of 4zxj.pdb_A SES surface, 4zxj.pdb_A SES surface, 1834 atoms,
2084 residues, 1560 bonds, 2076 pseudobonds  

> hide sel surfaces

Drag select of 1834 atoms, 2084 residues, 1560 bonds, 2076 pseudobonds  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  
Drag select of 1834 atoms, 2084 residues, 1560 bonds, 2076 pseudobonds  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> volume style surface

No volumes specified  
Drag select of 1834 atoms, 2084 residues, 1560 bonds, 2076 pseudobonds  

> volume style surface

No volumes specified  

> volume showOutlineBox true

No volumes specified  

> ui mousemode right "mark plane"

> ui mousemode right "mark surface"

> ui mousemode right "mark center"

> ui mousemode right "mark point"

> marker #2 position 47.64,125.3,19.57 color yellow radius 1

Drag select of AF-O33185-F1-model_v2.pdb_A SES surface, 999 residues  

> ui mousemode right "mark maximum"

> ui mousemode right "mark surface"

> ui mousemode right "mark center"

> ui mousemode right "mark surface"

> ui mousemode right rotate

> ui mousemode right translate

> ui mousemode right zoom

> ui mousemode right "rotate selected models"

> ui mousemode right label

Drag select of AF-O33185-F1-model_v2.pdb_A SES surface, 999 residues  

> ui mousemode right "tape measure"

> ui mousemode right "play map series"

> ui mousemode right "map eraser"

> ui mousemode right clip

> ui mousemode right "bond rotation"

> ui mousemode right windowing

> ui mousemode right "rotate slab"

> ui mousemode right distance

> hide sel surfaces

> show sel atoms

> hide sel cartoons

> hide sel atoms

> show sel cartoons

> set bgColor white

> lighting simple

> lighting soft

> lighting full

> color sel byhetero

> color sel bychain

> select #1/A:168-208

290 atoms, 296 bonds, 41 residues, 1 model selected  

> select #1/A:168-208

290 atoms, 296 bonds, 41 residues, 1 model selected  

> select
> #1/A:41-46,51-55,70-74,102-107,144-149,168-174,285-287,290-292,301-306,329-334,465-469,472-475,500-504,524-527,545-548,562-565,586-588,613-621,624-631,653-656,679-682,702-706,729-733,751-757,764-767,785-790,815-820,830-833,841-844,847-851,857-862,867-869,872-874,889-899,902-911,937-940,969-973,978-981

1589 atoms, 1591 bonds, 199 residues, 1 model selected  

> select clear

> select #1/A:168-208

290 atoms, 296 bonds, 41 residues, 1 model selected  

> select #1/A:213

14 atoms, 15 bonds, 1 residue, 1 model selected  

> select #1/A:213-214

22 atoms, 23 bonds, 2 residues, 1 model selected  

> select #1/A:169

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/A:169

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/A:6

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select #1/A:6-29

189 atoms, 190 bonds, 24 residues, 1 model selected  

> select
> #1/A:6-29,81-84,92-98,117-119,122-140,150-162,185-187,190-205,212-222,224-237,241-257,264-276,279-282,294-296,314-321,338-341,345-363,389-396,403-440,450-460,476-493,509-521,534-541,550-558,578-582,589-591,594-596,632-645,663-676,688-697,709-712,737-746,863-865,876-885,919-927,955-959,984-991

2922 atoms, 2935 bonds, 385 residues, 1 model selected  

> select
> #1/A:41-46,51-55,70-74,102-107,144-149,168-174,285-287,290-292,301-306,329-334,465-469,472-475,500-504,524-527,545-548,562-565,586-588,613-621,624-631,653-656,679-682,702-706,729-733,751-757,764-767,785-790,815-820,830-833,841-844,847-851,857-862,867-869,872-874,889-899,902-911,937-940,969-973,978-981

1589 atoms, 1591 bonds, 199 residues, 1 model selected  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  
Drag select of 999 residues  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> help help:user/tools/toolbar.html

> ui mousemode right "color key"

> key delete

> ui mousemode right distance

> ui mousemode right pivot

> ui mousemode right translate

> select clear

> nucleotides stubs

Drag select of 1835 atoms, 2084 residues, 1560 bonds, 2076 pseudobonds  

> nucleotides sel ladder

> hide sel cartoons

> select clear

Drag select of 5631 atoms, 5420 bonds, 2080 pseudobonds  

> rainbow sel

> color sel bychain

> color sel byhetero

> select clear

Drag select of 5631 atoms, 5420 bonds, 2080 pseudobonds  

> hide sel atoms

> show sel cartoons

Drag select of 1064 residues, 1348 pseudobonds  

> select #3/A:4 #4/A:4

10 atoms, 8 bonds, 2 residues, 2 models selected  

> select #3/A:4-53 #4/A:4-53

684 atoms, 702 bonds, 76 pseudobonds, 100 residues, 3 models selected  
Seqview [ID: 1] region 2 chains [1-50] RMSD: 0.000  
  

> select clear

> select #3/A:4-5 #4/A:4-5

20 atoms, 18 bonds, 4 residues, 2 models selected  

> select #3/A:4-1045 #4/A:4-1045

15606 atoms, 15988 bonds, 2024 pseudobonds, 2084 residues, 3 models selected  
Seqview [ID: 1] region 2 chains [1-1042] RMSD: 0.000  
  

> show sel cartoons

> color sel byhetero

> hide sel atoms

> color sel bychain

> color sel bynucleotide

> ui mousemode right "mark surface"

> select protein

23168 atoms, 23713 bonds, 2024 pseudobonds, 3083 residues, 4 models selected  

> select clear

Drag select of 2084 residues, 1348 pseudobonds  

> color (#!3-4 & sel) cornflower blue

> select clear

Drag select of 2084 residues, 1348 pseudobonds  

> label (#!3-4 & sel) atoms attribute element

> view sel

> select clear

> ui tool show H-Bonds

> hbonds color #00ffff reveal true

4553 hydrogen bonds found  
Drag select of 3303 atoms, 2535 residues, 2806 bonds, 4055 pseudobonds  
Drag select of 561 atoms, 443 residues, 474 bonds, 373 pseudobonds  

> select #1/A:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:1-700

5316 atoms, 5425 bonds, 630 pseudobonds, 700 residues, 2 models selected  

> select #1/A:26-50

182 atoms, 185 bonds, 5 pseudobonds, 25 residues, 2 models selected  

> select #1/A:26-50

182 atoms, 185 bonds, 5 pseudobonds, 25 residues, 2 models selected  

> select #1/A:1-25

194 atoms, 195 bonds, 16 pseudobonds, 25 residues, 2 models selected  

> select #1/A:1-25

194 atoms, 195 bonds, 16 pseudobonds, 25 residues, 2 models selected  

> select #1/A:4-29

205 atoms, 206 bonds, 20 pseudobonds, 26 residues, 2 models selected  

> select #1/A:4-29

205 atoms, 206 bonds, 20 pseudobonds, 26 residues, 2 models selected  

> select #1/A:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:1-999

7562 atoms, 7725 bonds, 879 pseudobonds, 999 residues, 2 models selected  

> show sel cartoons

> hide sel cartoons

> hide sel atoms

> show sel cartoons

> set bgColor black

Drag select of 2732 atoms, 2084 residues, 2324 bonds, 3674 pseudobonds  

> hide sel atoms

> select clear

> cartoon

> view

> hide atoms

Drag select of 999 residues, 561 pseudobonds  

> hide sel cartoons

> show sel cartoons

> select clear

> select #3/A:4-23 #4/A:4-23

270 atoms, 276 bonds, 36 pseudobonds, 40 residues, 3 models selected  

> select #3/A:4-143 #4/A:4-143

2070 atoms, 2128 bonds, 344 pseudobonds, 280 residues, 3 models selected  
Seqview [ID: 1] region 2 chains [1-140] RMSD: 0.000  
  

> select #3/A:4-23 #4/A:4-23

270 atoms, 276 bonds, 36 pseudobonds, 40 residues, 3 models selected  

> select #3/A:4-443 #4/A:4-443

6538 atoms, 6706 bonds, 1320 pseudobonds, 880 residues, 3 models selected  
Seqview [ID: 1] region 2 chains [1-440] RMSD: 0.000  
  

> select clear

> ui dockable true "Sequence Viewer"

> graphics silhouettes true

> set bgColor white

> set bgColor gray

> view

> ui mousemode right "mark surface"

> ui mousemode right "tape measure"

> select clear

Drag select of 2084 residues, 2192 pseudobonds  

> ui mousemode right "tape measure"

> ui mousemode right "pick blobs"

> ui mousemode right "play map series"

> select clear

> ui mousemode right "next docked"

Drag select of 2084 residues, 2192 pseudobonds  

> ui mousemode right "next docked"

QMainWindowLayout::tabPosition called with out-of-bounds value '0'  


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

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 - Build 10.18.10.4252
OpenGL renderer: Intel(R) HD Graphics
OpenGL vendor: Intel
Manufacturer: Dell Inc.
Model: OptiPlex 7010
OS: Microsoft Windows 10 Pro (Build 19044)
Memory: 8,470,966,272
MaxProcessMemory: 137,438,953,344
CPU: 2 Intel(R) Celeron(R) CPU G1620 @ 2.70GHz
OSLanguage: en-US
Locale: ('fr_FR', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 228
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

[pett]

There are several sequence errors before the crash as well (which I would need data for to reproduce), but they seem unlikely to have caused the crash.