AL2CO failure on Windows

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:\\\Users\\\Administrator\\\Documents\\\WeChat
> Files\\\wxid_nqiqweac2rnh22\\\FileStorage\\\File\\\2025-04\\\8i7s.cif"

8i7s.cif title:  
The crystal structure of human abl1 kinase domain in complex with ABL1-B1
[more info...]  
  
Chain information for 8i7s.cif #1  
---  
Chain | Description | UniProt  
A B | Tyrosine-protein kinase ABL1 | ABL1_HUMAN 229-500  
  
Non-standard residues in 8i7s.cif #1  
---  
6CI — 5-[3-(2-methoxy-5-oxidanyl-
phenyl)-1H-pyrrolo[2,3-b]pyridin-5-yl]-N,N-dimethyl-pyridine-3-carboxamide  
  
8i7s.cif mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> ui tool show "Blast Protein"

> blastprotein /B database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 version
> None name bp1

Webservices job id: IXM27033QQI9GHZL  
Alignment identifier is bp1 [1]  
Associated 8i7s.cif chain A to 4XEY_A with 0 mismatches  
Associated 8i7s.cif chain B to 4XEY_A with 0 mismatches  
Traceback (most recent call last):  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\blastprotein\ui\results.py", line 283, in <lambda>  
lambda: self._show_mav(self.table.selected)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\blastprotein\ui\results.py", line 617, in _show_mav  
self.session.alignments.new_alignment(seqs, name)  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\seqalign\manager.py", line 253, in new_alignment  
alignment = Alignment(self.session, seqs, identify_as, attrs, markups,
auto_destroy,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 147, in __init__  
self._headers = [hdr_class(self) for hdr_class in
session.alignments.headers()]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 147, in <listcomp>  
self._headers = [hdr_class(self) for hdr_class in
session.alignments.headers()]  
^^^^^^^^^^^^^^^  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 53, in __init__  
super().__init__(alignment, *args, eval_while_hidden=True, **kw)  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 70, in __init__  
self.reevaluate()  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 196, in reevaluate  
return super().reevaluate(pos1, pos2, evaluation_func=evaluation_func)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 220, in
reevaluate  
evaluation_func(pos1, pos2)  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 318, in
_reeval_al2co  
result = subprocess.run(command, capture_output=True, text=True, check=True)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\software\ChimeraX 1.9\bin\Lib\subprocess.py", line 571, in run  
raise CalledProcessError(retcode, process.args,  
subprocess.CalledProcessError: Command '['D:\\\software\\\ChimeraX
1.9\\\bin\\\Lib\\\site-
packages\\\chimerax\\\alignment_headers\\\bin\\\al2co.exe', '-i',
'C:\\\Users\\\Administrator\\\AppData\\\Local\\\Temp\\\tmp7mhjb3l3.aln', '-f',
'2', '-c', '0', '-w', '1', '-g', '0.5']' returned non-zero exit status 1.  
  
subprocess.CalledProcessError: Command '['D:\\\software\\\ChimeraX
1.9\\\bin\\\Lib\\\site-
packages\\\chimerax\\\alignment_headers\\\bin\\\al2co.exe', '-i',
'C:\\\Users\\\Administrator\\\AppData\\\Local\\\Temp\\\tmp7mhjb3l3.aln', '-f',
'2', '-c', '0', '-w', '1', '-g', '0.5']' returned non-zero exit status 1.  
  
File "D:\software\ChimeraX 1.9\bin\Lib\subprocess.py", line 571, in run  
raise CalledProcessError(retcode, process.args,  
  
See log for complete Python traceback.  
  
Alignment identifier is bp1 [2]  
Associated 8i7s.cif chain A to 4XEY_A with 0 mismatches  
Associated 8i7s.cif chain B to 4XEY_A with 0 mismatches  
Traceback (most recent call last):  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\blastprotein\ui\results.py", line 283, in <lambda>  
lambda: self._show_mav(self.table.selected)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\blastprotein\ui\results.py", line 617, in _show_mav  
self.session.alignments.new_alignment(seqs, name)  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\seqalign\manager.py", line 253, in new_alignment  
alignment = Alignment(self.session, seqs, identify_as, attrs, markups,
auto_destroy,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 147, in __init__  
self._headers = [hdr_class(self) for hdr_class in
session.alignments.headers()]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 147, in <listcomp>  
self._headers = [hdr_class(self) for hdr_class in
session.alignments.headers()]  
^^^^^^^^^^^^^^^  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 53, in __init__  
super().__init__(alignment, *args, eval_while_hidden=True, **kw)  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 70, in __init__  
self.reevaluate()  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 196, in reevaluate  
return super().reevaluate(pos1, pos2, evaluation_func=evaluation_func)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 220, in
reevaluate  
evaluation_func(pos1, pos2)  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 318, in
_reeval_al2co  
result = subprocess.run(command, capture_output=True, text=True, check=True)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\software\ChimeraX 1.9\bin\Lib\subprocess.py", line 571, in run  
raise CalledProcessError(retcode, process.args,  
subprocess.CalledProcessError: Command '['D:\\\software\\\ChimeraX
1.9\\\bin\\\Lib\\\site-
packages\\\chimerax\\\alignment_headers\\\bin\\\al2co.exe', '-i',
'C:\\\Users\\\Administrator\\\AppData\\\Local\\\Temp\\\tmp3bctray2.aln', '-f',
'2', '-c', '0', '-w', '1', '-g', '0.5']' returned non-zero exit status 1.  
  
subprocess.CalledProcessError: Command '['D:\\\software\\\ChimeraX
1.9\\\bin\\\Lib\\\site-
packages\\\chimerax\\\alignment_headers\\\bin\\\al2co.exe', '-i',
'C:\\\Users\\\Administrator\\\AppData\\\Local\\\Temp\\\tmp3bctray2.aln', '-f',
'2', '-c', '0', '-w', '1', '-g', '0.5']' returned non-zero exit status 1.  
  
File "D:\software\ChimeraX 1.9\bin\Lib\subprocess.py", line 571, in run  
raise CalledProcessError(retcode, process.args,  
  
See log for complete Python traceback.  
  

> open pdb:4XEY

4xey title:  
Crystal structure of an SH2-kinase domain construct of c-Abl tyrosine kinase
[more info...]  
  
Chain information for 4xey #2  
---  
Chain | Description | UniProt  
A B | Tyrosine-protein kinase ABL1 | ABL1_HUMAN 138-534  
  
Non-standard residues in 4xey #2  
---  
1N1 —
N-(2-chloro-6-methylphenyl)-2-({6-[4-(2-hydroxyethyl)piperazin-1-yl]-2-methylpyrimidin-4-yl}amino)-1,3-thiazole-5-carboxamide
(Dasatinib)  
  
4xey mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
Associated 4xey chain B to 4XEY_A with 0 mismatches  
Associated 4xey chain A to 4XEY_A with 0 mismatches  
Associated 4xey chain B to 4XEY_A with 0 mismatches  
Associated 4xey chain A to 4XEY_A with 0 mismatches  

> matchmaker #2/A to #1/B

Computing secondary structure  
[Repeated 1 time(s)]  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 8i7s.cif, chain B (#1) with 4XEY_A, chain A (#2), sequence
alignment score = 1358.9  
RMSD between 257 pruned atom pairs is 0.689 angstroms; (across all 260 pairs:
0.974)  
  
Alignment identifier is bp1 [3]  
Associated 8i7s.cif chain A to 4XEY_A with 0 mismatches  
Associated 8i7s.cif chain B to 4XEY_A with 0 mismatches  
Associated 4XEY_A chain B to 4XEY_A with 0 mismatches  
Associated 4XEY_A chain A to 4XEY_A with 0 mismatches  
Traceback (most recent call last):  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\blastprotein\ui\results.py", line 283, in <lambda>  
lambda: self._show_mav(self.table.selected)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\blastprotein\ui\results.py", line 617, in _show_mav  
self.session.alignments.new_alignment(seqs, name)  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\seqalign\manager.py", line 253, in new_alignment  
alignment = Alignment(self.session, seqs, identify_as, attrs, markups,
auto_destroy,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 147, in __init__  
self._headers = [hdr_class(self) for hdr_class in
session.alignments.headers()]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 147, in <listcomp>  
self._headers = [hdr_class(self) for hdr_class in
session.alignments.headers()]  
^^^^^^^^^^^^^^^  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 53, in __init__  
super().__init__(alignment, *args, eval_while_hidden=True, **kw)  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 70, in __init__  
self.reevaluate()  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 196, in reevaluate  
return super().reevaluate(pos1, pos2, evaluation_func=evaluation_func)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 220, in
reevaluate  
evaluation_func(pos1, pos2)  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 318, in
_reeval_al2co  
result = subprocess.run(command, capture_output=True, text=True, check=True)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\software\ChimeraX 1.9\bin\Lib\subprocess.py", line 571, in run  
raise CalledProcessError(retcode, process.args,  
subprocess.CalledProcessError: Command '['D:\\\software\\\ChimeraX
1.9\\\bin\\\Lib\\\site-
packages\\\chimerax\\\alignment_headers\\\bin\\\al2co.exe', '-i',
'C:\\\Users\\\Administrator\\\AppData\\\Local\\\Temp\\\tmpkprkizqy.aln', '-f',
'2', '-c', '0', '-w', '1', '-g', '0.5']' returned non-zero exit status 1.  
  
subprocess.CalledProcessError: Command '['D:\\\software\\\ChimeraX
1.9\\\bin\\\Lib\\\site-
packages\\\chimerax\\\alignment_headers\\\bin\\\al2co.exe', '-i',
'C:\\\Users\\\Administrator\\\AppData\\\Local\\\Temp\\\tmpkprkizqy.aln', '-f',
'2', '-c', '0', '-w', '1', '-g', '0.5']' returned non-zero exit status 1.  
  
File "D:\software\ChimeraX 1.9\bin\Lib\subprocess.py", line 571, in run  
raise CalledProcessError(retcode, process.args,  
  
See log for complete Python traceback.  
  
Alignment identifier is bp1 [4]  
Associated 8i7s.cif chain A to 4XEY_A with 0 mismatches  
Associated 8i7s.cif chain B to 4XEY_A with 0 mismatches  
Associated 4XEY_A chain B to 4XEY_A with 0 mismatches  
Associated 4XEY_A chain A to 4XEY_A with 0 mismatches  
Traceback (most recent call last):  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\blastprotein\ui\results.py", line 283, in <lambda>  
lambda: self._show_mav(self.table.selected)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\blastprotein\ui\results.py", line 617, in _show_mav  
self.session.alignments.new_alignment(seqs, name)  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\seqalign\manager.py", line 253, in new_alignment  
alignment = Alignment(self.session, seqs, identify_as, attrs, markups,
auto_destroy,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 147, in __init__  
self._headers = [hdr_class(self) for hdr_class in
session.alignments.headers()]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 147, in <listcomp>  
self._headers = [hdr_class(self) for hdr_class in
session.alignments.headers()]  
^^^^^^^^^^^^^^^  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 53, in __init__  
super().__init__(alignment, *args, eval_while_hidden=True, **kw)  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 70, in __init__  
self.reevaluate()  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 196, in reevaluate  
return super().reevaluate(pos1, pos2, evaluation_func=evaluation_func)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 220, in
reevaluate  
evaluation_func(pos1, pos2)  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 318, in
_reeval_al2co  
result = subprocess.run(command, capture_output=True, text=True, check=True)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\software\ChimeraX 1.9\bin\Lib\subprocess.py", line 571, in run  
raise CalledProcessError(retcode, process.args,  
subprocess.CalledProcessError: Command '['D:\\\software\\\ChimeraX
1.9\\\bin\\\Lib\\\site-
packages\\\chimerax\\\alignment_headers\\\bin\\\al2co.exe', '-i',
'C:\\\Users\\\Administrator\\\AppData\\\Local\\\Temp\\\tmp11walai3.aln', '-f',
'2', '-c', '0', '-w', '1', '-g', '0.5']' returned non-zero exit status 1.  
  
subprocess.CalledProcessError: Command '['D:\\\software\\\ChimeraX
1.9\\\bin\\\Lib\\\site-
packages\\\chimerax\\\alignment_headers\\\bin\\\al2co.exe', '-i',
'C:\\\Users\\\Administrator\\\AppData\\\Local\\\Temp\\\tmp11walai3.aln', '-f',
'2', '-c', '0', '-w', '1', '-g', '0.5']' returned non-zero exit status 1.  
  
File "D:\software\ChimeraX 1.9\bin\Lib\subprocess.py", line 571, in run  
raise CalledProcessError(retcode, process.args,  
  
See log for complete Python traceback.  
  
Alignment identifier is bp1 [5]  
Associated 8i7s.cif chain A to 4XEY_A with 0 mismatches  
Associated 8i7s.cif chain B to 4XEY_A with 0 mismatches  
Associated 4XEY_A chain B to 4XEY_A with 0 mismatches  
Associated 4XEY_A chain A to 4XEY_A with 0 mismatches  
Traceback (most recent call last):  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\blastprotein\ui\results.py", line 283, in <lambda>  
lambda: self._show_mav(self.table.selected)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\blastprotein\ui\results.py", line 617, in _show_mav  
self.session.alignments.new_alignment(seqs, name)  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\seqalign\manager.py", line 253, in new_alignment  
alignment = Alignment(self.session, seqs, identify_as, attrs, markups,
auto_destroy,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 147, in __init__  
self._headers = [hdr_class(self) for hdr_class in
session.alignments.headers()]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 147, in <listcomp>  
self._headers = [hdr_class(self) for hdr_class in
session.alignments.headers()]  
^^^^^^^^^^^^^^^  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 53, in __init__  
super().__init__(alignment, *args, eval_while_hidden=True, **kw)  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 70, in __init__  
self.reevaluate()  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 196, in reevaluate  
return super().reevaluate(pos1, pos2, evaluation_func=evaluation_func)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 220, in
reevaluate  
evaluation_func(pos1, pos2)  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 318, in
_reeval_al2co  
result = subprocess.run(command, capture_output=True, text=True, check=True)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\software\ChimeraX 1.9\bin\Lib\subprocess.py", line 571, in run  
raise CalledProcessError(retcode, process.args,  
subprocess.CalledProcessError: Command '['D:\\\software\\\ChimeraX
1.9\\\bin\\\Lib\\\site-
packages\\\chimerax\\\alignment_headers\\\bin\\\al2co.exe', '-i',
'C:\\\Users\\\Administrator\\\AppData\\\Local\\\Temp\\\tmpehzbmk69.aln', '-f',
'2', '-c', '0', '-w', '1', '-g', '0.5']' returned non-zero exit status 1.  
  
subprocess.CalledProcessError: Command '['D:\\\software\\\ChimeraX
1.9\\\bin\\\Lib\\\site-
packages\\\chimerax\\\alignment_headers\\\bin\\\al2co.exe', '-i',
'C:\\\Users\\\Administrator\\\AppData\\\Local\\\Temp\\\tmpehzbmk69.aln', '-f',
'2', '-c', '0', '-w', '1', '-g', '0.5']' returned non-zero exit status 1.  
  
File "D:\software\ChimeraX 1.9\bin\Lib\subprocess.py", line 571, in run  
raise CalledProcessError(retcode, process.args,  
  
See log for complete Python traceback.  
  
Alignment identifier is bp1 [6]  
Associated 8i7s.cif chain A to 4XEY_A with 0 mismatches  
Associated 8i7s.cif chain B to 4XEY_A with 0 mismatches  
Associated 4XEY_A chain B to 4XEY_A with 0 mismatches  
Associated 4XEY_A chain A to 4XEY_A with 0 mismatches  
Traceback (most recent call last):  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\blastprotein\ui\results.py", line 283, in <lambda>  
lambda: self._show_mav(self.table.selected)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\blastprotein\ui\results.py", line 617, in _show_mav  
self.session.alignments.new_alignment(seqs, name)  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\seqalign\manager.py", line 253, in new_alignment  
alignment = Alignment(self.session, seqs, identify_as, attrs, markups,
auto_destroy,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 147, in __init__  
self._headers = [hdr_class(self) for hdr_class in
session.alignments.headers()]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 147, in <listcomp>  
self._headers = [hdr_class(self) for hdr_class in
session.alignments.headers()]  
^^^^^^^^^^^^^^^  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 53, in __init__  
super().__init__(alignment, *args, eval_while_hidden=True, **kw)  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 70, in __init__  
self.reevaluate()  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 196, in reevaluate  
return super().reevaluate(pos1, pos2, evaluation_func=evaluation_func)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 220, in
reevaluate  
evaluation_func(pos1, pos2)  
File "D:\software\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 318, in
_reeval_al2co  
result = subprocess.run(command, capture_output=True, text=True, check=True)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\software\ChimeraX 1.9\bin\Lib\subprocess.py", line 571, in run  
raise CalledProcessError(retcode, process.args,  
subprocess.CalledProcessError: Command '['D:\\\software\\\ChimeraX
1.9\\\bin\\\Lib\\\site-
packages\\\chimerax\\\alignment_headers\\\bin\\\al2co.exe', '-i',
'C:\\\Users\\\Administrator\\\AppData\\\Local\\\Temp\\\tmpq0zn5t2a.aln', '-f',
'2', '-c', '0', '-w', '1', '-g', '0.5']' returned non-zero exit status 1.  
  
subprocess.CalledProcessError: Command '['D:\\\software\\\ChimeraX
1.9\\\bin\\\Lib\\\site-
packages\\\chimerax\\\alignment_headers\\\bin\\\al2co.exe', '-i',
'C:\\\Users\\\Administrator\\\AppData\\\Local\\\Temp\\\tmpq0zn5t2a.aln', '-f',
'2', '-c', '0', '-w', '1', '-g', '0.5']' returned non-zero exit status 1.  
  
File "D:\software\ChimeraX 1.9\bin\Lib\subprocess.py", line 571, in run  
raise CalledProcessError(retcode, process.args,  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 560.94
OpenGL renderer: NVIDIA GeForce RTX 3050/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: zh_CN.cp936
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows

Manufacturer: Colorful Technology And Development Co.,LTD
Model: H610M-D EVO
OS: Microsoft Windows 10 专业版 (Build 19045)
Memory: 16,981,962,752
MaxProcessMemory: 137,438,953,344
CPU: 12 12th Gen Intel(R) Core(TM) i5-12400F
OSLanguage: zh-CN

Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2024.8.30
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    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: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.5
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pywin32: 306
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    WMI: 1.5.1