The following bug report has been submitted:
Platform: Windows-10-10.0.22631
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
2025-08-28 10:23:00,798 WARNING Retrying (Retry(total=2, connect=None,
read=None, redirect=None, status=None)) after connection broken by
'NameResolutionError("<urllib3.connection.HTTPConnection object at
0x000001D9CA263C10>: Failed to resolve 'webservices.rbvi.ucsf.edu' ([Errno
11001] getaddrinfo failed)")':
/cxservices/api/v1/chimerax/updates?uuid=c58977d8-b2ec-5207-8f03-9dd7e8ebe31b&OS=windows&OSVersion=10.0.22631&ChimeraXVersion=1.8
2025-08-28 10:23:00,802 WARNING Retrying (Retry(total=1, connect=None,
read=None, redirect=None, status=None)) after connection broken by
'NameResolutionError("<urllib3.connection.HTTPConnection object at
0x000001D9CA270550>: Failed to resolve 'webservices.rbvi.ucsf.edu' ([Errno
11001] getaddrinfo failed)")':
/cxservices/api/v1/chimerax/updates?uuid=c58977d8-b2ec-5207-8f03-9dd7e8ebe31b&OS=windows&OSVersion=10.0.22631&ChimeraXVersion=1.8
2025-08-28 10:23:00,804 WARNING Retrying (Retry(total=0, connect=None,
read=None, redirect=None, status=None)) after connection broken by
'NameResolutionError("<urllib3.connection.HTTPConnection object at
0x000001D9CA271650>: Failed to resolve 'webservices.rbvi.ucsf.edu' ([Errno
11001] getaddrinfo failed)")':
/cxservices/api/v1/chimerax/updates?uuid=c58977d8-b2ec-5207-8f03-9dd7e8ebe31b&OS=windows&OSVersion=10.0.22631&ChimeraXVersion=1.8
"Unable to open monitor interface to \\\\\\\\.\\\DISPLAY2:" "The operation
completed successfully."
"Unable to open monitor interface to \\\\\\\\.\\\DISPLAY3:" "The operation
completed successfully."
> open C:/Users/Tsung-ITsai/Downloads/huMUC13_SEA_C14/model_1.cif
model_1.cif title:
Chai-1 predicted structure [more info...]
Chain information for model_1.cif #1
---
Chain | Description
A | Entity A
B | Entity B
Color model_1.cif by residue attribute pLDDT_score
> color bychain
> set bgColor white
> lighting full
Alignment identifier is 1/A
Alignment identifier is 1/B
> select /A:77
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:77-86
77 atoms, 78 bonds, 10 residues, 1 model selected
> show sel atoms
> select /A:121
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:121-151
243 atoms, 244 bonds, 31 residues, 1 model selected
> show sel atoms
> select clear
> select /A:142
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:142-145
24 atoms, 23 bonds, 4 residues, 1 model selected
> select clear
> open C:/Users/Tsung-ITsai/Downloads/cyMUC13_SEA_C14/model_1.cif
model_1.cif title:
Chai-1 predicted structure [more info...]
Chain information for model_1.cif #2
---
Chain | Description
A | Entity A
B | Entity B
Color model_1.cif by residue attribute pLDDT_score
> color bychain
> align #1 toAtoms #2
Unequal number of atoms to pair, 3652 and 3645
> select clear
> align #1 toAtoms #2
Unequal number of atoms to pair, 3652 and 3645
> hide #2 models
> select #1/A:140
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:140-147
62 atoms, 62 bonds, 8 residues, 1 model selected
> select clear
> show #2 models
> hide #2 models
> hide #1 models
> show #2 models
> select /A
3793 atoms, 3864 bonds, 500 residues, 2 models selected
> align #1/A #2/A
Missing required "to_atoms" argument
> align #1/A toAtoms #2/A
Unequal number of atoms to pair, 1900 and 1893
> show #1 models
> select clear
> align #1/A toAtoms #2/A
Unequal number of atoms to pair, 1900 and 1893
> align #1/A toAtoms #2/B
Unequal number of atoms to pair, 1900 and 1752
> hide #2 models
"Unable to open monitor interface to \\\\\\\\.\\\DISPLAY1:" "The operation
completed successfully."
[Repeated 2 time(s)]
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
"Unable to open monitor interface to \\\\\\\\.\\\DISPLAY2:" "The operation
completed successfully."
"Unable to open monitor interface to \\\\\\\\.\\\DISPLAY3:" "The operation
completed successfully."
"Unable to open monitor interface to \\\\\\\\.\\\DISPLAY2:" "The operation
completed successfully."
"Unable to open monitor interface to \\\\\\\\.\\\DISPLAY3:" "The operation
completed successfully."
"Unable to open monitor interface to \\\\\\\\.\\\DISPLAY2:" "The operation
completed successfully."
"Unable to open monitor interface to \\\\\\\\.\\\DISPLAY3:" "The operation
completed successfully."
> close
> open C:/Users/Tsung-ITsai/Downloads/huMUC13_SEA_C14/model_1.cif
model_1.cif title:
Chai-1 predicted structure [more info...]
Chain information for model_1.cif #1
---
Chain | Description
A | Entity A
B | Entity B
Color model_1.cif by residue attribute pLDDT_score
> set bgColor white
> color bychain
Alignment identifier is 1/A
Alignment identifier is 1/B
> contacts #1/A restrict #1/B saveFile AB_contacts.txt log true reveal true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
89 contacts
atom1 atom2 overlap distance
/A ALA 108 CB /B LYS 181 NZ 0.789 2.731
/A SER 143 CA /B TRP 219 CE3 0.571 3.069
/A SER 144 N /B TRP 219 CE3 0.534 2.866
/A ALA 108 CB /B LYS 181 CE 0.523 3.237
/A SER 143 C /B TRP 219 CZ3 0.522 2.848
/A SER 143 C /B TRP 219 CE3 0.384 2.986
/A LYS 138 NZ /B ASP 57 OD2 0.373 2.287
/A SER 143 CA /B TRP 219 CZ3 0.365 3.275
/A LYS 138 NZ /B ASP 55 CG 0.350 3.170
/A SER 144 CB /B TRP 219 CE2 0.323 3.167
/A SER 144 N /B TRP 219 CZ3 0.319 3.081
/A LYS 138 NZ /B ASP 57 CG 0.264 3.256
/A SER 143 CB /B TRP 219 O 0.241 3.059
/A SER 142 CA /B TRP 33 NE1 0.234 3.286
/A LYS 138 CE /B TRP 33 CZ2 0.167 3.473
/A ALA 108 CB /B LYS 181 CD 0.164 3.596
/A SER 142 CA /B TRP 33 CD1 0.158 3.482
/A LYS 138 NZ /B ASP 55 OD2 0.143 2.517
/A ASP 110 OD2 /B LYS 181 CE 0.140 3.160
/A SER 144 CB /B TRP 219 CZ2 0.120 3.520
/A SER 144 CB /B TRP 219 CD2 0.118 3.372
/A ARG 107 NH1 /B ASP 178 OD2 0.118 2.542
/A SER 144 CB /B TRP 219 NE1 0.070 3.450
/A SER 143 O /B TRP 219 CZ3 0.068 3.112
/A ASP 110 CG /B LYS 181 CE 0.044 3.716
/A SER 142 CB /B TRP 33 NE1 0.016 3.504
/A SER 143 CA /B TRP 219 O 0.013 3.287
/A SER 142 O /B PHE 224 CZ -0.000 3.180
/A SER 144 N /B TRP 219 CD2 -0.017 3.267
/A LYS 138 NZ /B ASP 57 CB -0.023 3.543
/A ARG 141 C /B TRP 33 CD1 -0.043 3.413
/A ARG 107 NH1 /B TYR 177 CE2 -0.055 3.455
/A LYS 138 CE /B TYR 52 CD2 -0.056 3.696
/A SER 144 CA /B TRP 219 CZ3 -0.068 3.708
/A LYS 138 CD /B TYR 52 CD2 -0.073 3.713
/A ASP 110 CG /B LYS 181 NZ -0.074 3.594
/A ARG 141 O /B TRP 33 CD1 -0.077 3.257
/A LYS 138 CD /B TYR 52 CE2 -0.088 3.728
/A LYS 138 CG /B TRP 33 CZ2 -0.104 3.744
/A THR 53 CG2 /B TYR 160 OH -0.110 3.450
/A SER 144 CA /B TRP 219 CE3 -0.114 3.754
/A SER 142 N /B TRP 33 NE1 -0.114 3.394
/A SER 144 CB /B HIS 162 NE2 -0.118 3.638
/A SER 142 N /B TRP 33 CD1 -0.121 3.521
/A SER 144 CA /B TRP 219 CH2 -0.125 3.765
/A LYS 138 CE /B TRP 33 CH2 -0.128 3.768
/A SER 144 CB /B TRP 219 CD1 -0.143 3.783
/A ARG 141 NH1 /B THR 31 CB -0.144 3.664
/A ARG 107 NH1 /B ASP 178 CG -0.148 3.668
/A SER 144 N /B TRP 219 O -0.154 2.814
/A SER 145 O /B TYR 160 CE2 -0.157 3.337
/A SER 144 CA /B TRP 219 CZ2 -0.179 3.819
/A SER 144 OG /B TYR 160 CD2 -0.185 3.405
/A SER 144 O /B SER 220 CA -0.193 3.493
/A ARG 141 CD /B THR 31 O -0.209 3.509
/A SER 142 CB /B TRP 33 CE2 -0.215 3.705
/A ILE 140 CG2 /B TRP 100 CH2 -0.216 3.856
/A SER 142 CB /B TRP 33 CZ2 -0.225 3.865
/A SER 143 N /B TRP 219 CZ3 -0.242 3.642
/A ARG 107 CZ /B ASP 178 OD2 -0.245 3.275
/A LYS 138 O /B TRP 33 NE1 -0.247 2.907
/A ARG 107 NE /B TRP 100 CZ2 -0.251 3.651
/A LYS 138 CG /B TYR 52 CE1 -0.253 3.893
/A SER 144 OG /B TYR 160 CB -0.254 3.594
/A LYS 138 CE /B TYR 52 CB -0.256 4.016
/A ASN 146 OD1 /B THR 159 CG2 -0.266 3.566
/A ARG 107 NH1 /B TYR 177 CD2 -0.272 3.672
/A SER 144 CB /B TRP 219 CE3 -0.278 3.918
/A SER 144 N /B TRP 219 CH2 -0.281 3.681
/A THR 53 CB /B TYR 160 OH -0.282 3.622
/A ARG 141 CA /B TRP 100 CE3 -0.285 3.925
/A SER 144 CA /B TRP 219 CD2 -0.289 3.779
/A ASN 146 ND2 /B THR 159 CG2 -0.290 3.810
/A SER 144 CB /B TRP 219 CG -0.293 3.783
/A SER 144 O /B SER 220 CB -0.302 3.602
/A SER 143 C /B TRP 219 CH2 -0.311 3.681
/A LYS 138 CE /B ASP 55 OD2 -0.319 3.619
/A SER 144 CA /B TRP 219 CE2 -0.327 3.817
/A LEU 148 O /B TRP 100 CZ2 -0.329 3.509
/A SER 142 CA /B TRP 33 CE2 -0.330 3.820
/A LYS 138 CE /B TYR 52 CG -0.332 3.822
/A LYS 138 CE /B ASP 57 OD2 -0.340 3.640
/A ASP 110 OD2 /B LYS 181 NZ -0.344 3.004
/A ARG 141 CB /B TRP 33 CD1 -0.351 3.991
/A SER 144 CB /B TRP 219 CH2 -0.356 3.996
/A ARG 141 CD /B TYR 32 CE1 -0.369 4.009
/A ASN 146 CG /B THR 159 CG2 -0.372 3.862
/A LYS 138 CG /B TYR 52 CD1 -0.380 4.020
/A ARG 107 NH2 /B ASP 178 CG -0.388 3.908
89 contacts
> contacts #1/A restrict #1/B distanceCutoff 4.0 saveFile AB_contacts_4A.txt
Expected a keyword
> graphics silhouettes true
> cd "C:/Users/Tsung-ITsai/OneDrive - IMMUNOME
> INC/Project_Immunome/ADC_009_MUC13/PDB/cyMUC13_SEA_C14"
Current working directory is: C:\Users\Tsung-ITsai\OneDrive - IMMUNOME
INC\Project_Immunome\ADC_009_MUC13\PDB\cyMUC13_SEA_C14
> contacts #1/A restrict #1/B distanceCutoff 4.0 saveFile AB_contacts_4A.txt
Expected a keyword
> contacts #1/A restrict #1/B distanceCutoff 4.0 saveFile C:\Users\Tsung-
> ITsai\OneDrive - IMMUNOME
> INC\Project_Immunome\ADC_009_MUC13\PDB\AB_contacts_4A.txt
Expected a keyword
> contacts #1/A restrict #1/B distanceCutoff 4.0 saveFile C:\Users\Tsung-
> ITsai\OneDrive - IMMUNOME
> INC\Project_Immunome\ADC_009_MUC13\PDB\AB_contacts_4A.txt
Expected a keyword
> contacts #1/A restrict #1/B distanceOnly 4.0 saveFile "C:\Users\Tsung-
> ITsai\OneDrive - IMMUNOME
> INC\Project_Immunome\ADC_009_MUC13\PDB\AB_contacts_4A.txt"
137 distances
> contacts #1/A restrict #1/B distanceOnly 4.0 saveFile "C:\Users\Tsung-
> ITsai\OneDrive - IMMUNOME
> INC\Project_Immunome\ADC_009_MUC13\PDB\AB_contacts_4A.csv"
137 distances
> contacts #1/A restrict #1/B distanceOnly 4.0 saveFile
> C:\path\AB_contacts_4A.csv format csv
Expected a keyword
> contacts #1/A restrict #1/B distanceOnly 4.0 saveFile "C:\Users\Tsung-
> ITsai\OneDrive - IMMUNOME
> INC\Project_Immunome\ADC_009_MUC13\PDB\AB_contacts_4A.csv" format csv
Expected a keyword
> contacts #1/A restrict #1/B distanceOnly 4.0 saveFile
> C:\path\AB_contacts_4A.csv format csv
Expected a keyword
> contacts #1/A restrict #1/B distanceOnly 4 saveFile
> C:\path\AB_contacts_4A.csv log true
Ignore distances between atoms separated by 4 bonds or less
Detect intra-residue distances: False
Detect intra-molecule distances: True
137 distances
atom1 atom2 distance
/A LYS 138 NZ /B ASP 57 OD2 2.287
/A LYS 138 NZ /B ASP 55 OD2 2.517
/A ARG 107 NH1 /B ASP 178 OD2 2.542
/A ALA 108 CB /B LYS 181 NZ 2.731
/A SER 144 N /B TRP 219 O 2.814
/A SER 143 C /B TRP 219 CZ3 2.848
/A SER 144 N /B TRP 219 CE3 2.866
/A LYS 138 O /B TRP 33 NE1 2.907
/A SER 143 C /B TRP 219 CE3 2.986
/A ASP 110 OD2 /B LYS 181 NZ 3.004
/A SER 143 CB /B TRP 219 O 3.059
/A ARG 141 NH1 /B THR 31 O 3.068
/A SER 143 CA /B TRP 219 CE3 3.069
/A SER 144 N /B TRP 219 CZ3 3.081
/A LYS 138 NZ /B ASP 55 OD1 3.107
/A SER 143 O /B TRP 219 CZ3 3.112
/A ASP 110 OD2 /B LYS 181 CE 3.160
/A SER 144 CB /B TRP 219 CE2 3.167
/A LYS 138 NZ /B ASP 55 CG 3.170
/A SER 142 O /B PHE 224 CZ 3.180
/A SER 142 O /B GLN 50 NE2 3.194
/A ASN 146 OD1 /B TYR 160 OH 3.201
/A ALA 108 CB /B LYS 181 CE 3.237
/A SER 144 OG /B HIS 162 NE2 3.250
/A LYS 138 NZ /B ASP 57 CG 3.256
/A ARG 141 O /B TRP 33 CD1 3.257
/A SER 144 N /B TRP 219 CD2 3.267
/A ARG 107 NH2 /B ASP 178 OD2 3.269
/A ARG 107 CZ /B ASP 178 OD2 3.275
/A SER 143 CA /B TRP 219 CZ3 3.275
/A SER 142 CA /B TRP 33 NE1 3.286
/A SER 143 CA /B TRP 219 O 3.287
/A ARG 107 O /B TYR 177 OH 3.318
/A SER 145 O /B TYR 160 CE2 3.337
/A SER 142 O /B GLN 50 OE1 3.365
/A SER 144 CB /B TRP 219 CD2 3.372
/A SER 144 O /B SER 220 OG 3.376
/A SER 142 N /B TRP 33 NE1 3.394
/A SER 144 OG /B TYR 160 CD2 3.405
/A ARG 141 C /B TRP 33 CD1 3.413
/A SER 144 CB /B TRP 219 NE1 3.450
/A THR 53 CG2 /B TYR 160 OH 3.450
/A ARG 107 NH1 /B TYR 177 CE2 3.455
/A LYS 138 CE /B TRP 33 CZ2 3.473
/A SER 142 OG /B GLN 50 OE1 3.476
/A SER 142 CA /B TRP 33 CD1 3.482
/A SER 144 O /B SER 220 CA 3.493
/A SER 142 CB /B TRP 33 NE1 3.504
/A LEU 148 O /B TRP 100 CZ2 3.509
/A ARG 141 CD /B THR 31 O 3.509
/A SER 144 CB /B TRP 219 CZ2 3.520
/A SER 142 N /B TRP 33 CD1 3.521
/A LYS 138 NZ /B ASP 57 CB 3.543
/A SER 143 C /B TRP 219 O 3.544
/A ASN 146 OD1 /B THR 159 CG2 3.566
/A ILE 140 O /B TRP 100 CZ3 3.583
/A SER 144 OG /B TYR 160 CB 3.594
/A ASP 110 CG /B LYS 181 NZ 3.594
/A ALA 108 CB /B LYS 181 CD 3.596
/A SER 144 O /B SER 220 CB 3.602
/A LYS 138 CE /B ASP 55 OD2 3.619
/A THR 53 CB /B TYR 160 OH 3.622
/A SER 144 CB /B HIS 162 NE2 3.638
/A LYS 138 CE /B ASP 57 OD2 3.640
/A SER 143 N /B TRP 219 CZ3 3.642
/A ARG 107 NE /B TRP 100 CZ2 3.651
/A SER 143 O /B TRP 219 CH2 3.659
/A ARG 141 NH1 /B THR 31 CB 3.664
/A ARG 107 NH1 /B ASP 178 CG 3.668
/A ARG 107 NH1 /B TYR 177 CD2 3.672
/A SER 142 O /B PHE 224 CE2 3.674
/A SER 143 C /B TRP 219 CH2 3.681
/A SER 144 N /B TRP 219 CH2 3.681
/A SER 142 O /B GLN 50 CD 3.685
/A LYS 138 CE /B TYR 52 CD2 3.696
/A SER 142 CB /B TRP 33 CE2 3.705
/A ARG 107 NH2 /B ASP 178 OD1 3.706
/A SER 144 CA /B TRP 219 CZ3 3.708
/A SER 144 N /B TRP 219 C 3.708
/A LYS 138 CD /B TYR 52 CD2 3.713
/A ASP 110 CG /B LYS 181 CE 3.716
/A SER 143 O /B TRP 219 CE3 3.722
/A LYS 138 CD /B TYR 52 CE2 3.728
/A ASP 110 OD1 /B LYS 181 NZ 3.730
/A PHE 147 O /B TRP 100 CH2 3.742
/A LYS 138 CG /B TRP 33 CZ2 3.744
/A ARG 141 C /B TRP 33 NE1 3.748
/A ARG 107 O /B TYR 177 CE2 3.750
/A SER 144 OG /B HIS 162 CE1 3.751
/A SER 144 CA /B TRP 219 CE3 3.754
/A SER 144 CA /B TRP 219 CH2 3.765
/A LYS 138 CE /B TRP 33 CH2 3.768
/A ASN 146 OD1 /B TYR 160 CZ 3.770
/A SER 144 CA /B TRP 219 CD2 3.779
/A SER 144 CB /B TRP 219 CG 3.783
/A SER 144 CB /B TRP 219 CD1 3.783
/A ASN 146 ND2 /B THR 159 CG2 3.810
/A SER 144 N /B TRP 219 CE2 3.816
/A SER 144 CA /B TRP 219 CE2 3.817
/A SER 143 N /B TRP 219 CE3 3.818
/A SER 144 CA /B TRP 219 CZ2 3.819
/A SER 142 CA /B TRP 33 CE2 3.820
/A LYS 138 CE /B TYR 52 CG 3.822
/A SER 145 C /B TYR 160 CE2 3.841
/A LYS 138 O /B TRP 33 CD1 3.851
/A ILE 140 CG2 /B TRP 100 CH2 3.856
/A SER 142 O /B TRP 219 CE3 3.857
/A ASN 146 CG /B THR 159 CG2 3.862
/A SER 144 CA /B TRP 219 O 3.863
/A SER 142 CB /B TRP 33 CZ2 3.865
/A LYS 138 O /B TRP 33 CE2 3.867
/A SER 143 C /B TRP 219 CD2 3.871
/A SER 144 CB /B TRP 219 O 3.880
/A SER 142 OG /B TRP 33 CZ2 3.881
/A LYS 138 CD /B ASP 55 OD2 3.886
/A LYS 138 CG /B TYR 52 CE1 3.893
/A ARG 107 NH2 /B ASP 178 CG 3.908
/A LYS 138 CE /B ASP 55 OD1 3.910
/A ASN 146 OD1 /B TYR 160 CE2 3.911
/A ARG 141 O /B TRP 219 CZ3 3.913
/A LEU 148 O /B TRP 100 CH2 3.917
/A LYS 138 CG /B TYR 52 CZ 3.918
/A SER 144 CB /B TRP 219 CE3 3.918
/A ARG 141 CA /B TRP 100 CE3 3.925
/A LYS 138 C /B TRP 33 NE1 3.925
/A SER 145 O /B TYR 160 CD2 3.941
/A SER 144 OG /B TYR 160 CG 3.947
/A SER 142 OG /B TRP 33 CE2 3.951
/A LYS 138 CG /B TRP 33 NE1 3.962
/A ARG 141 NH1 /B THR 31 OG1 3.968
/A SER 144 OG /B TRP 219 CE2 3.969
/A ARG 141 O /B TRP 33 NE1 3.979
/A ARG 107 O /B TYR 177 CZ 3.983
/A ARG 141 CB /B TRP 33 CD1 3.991
/A SER 144 OG /B TRP 219 NE1 3.993
/A SER 144 CB /B TRP 219 CH2 3.996
/A ARG 107 NE /B TRP 100 CH2 3.996
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\clashes\cmd.py", line 54, in cmd_contacts
return _cmd(session, test_atoms, name, hbond_allowance, overlap_cutoff,
"contacts", color, radius, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\clashes\cmd.py", line 161, in _cmd
_file_output(save_file, info, naming_style)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\clashes\cmd.py", line 245, in _file_output
out_file = open_output(file_name, 'utf-8')
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-packages\chimerax\io\io.py",
line 87, in open_output
return open(fs_output, mode, encoding=encoding)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory:
'C:\\\path\\\AB_contacts_4A.csv'
FileNotFoundError: [Errno 2] No such file or directory:
'C:\\\path\\\AB_contacts_4A.csv'
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-packages\chimerax\io\io.py",
line 87, in open_output
return open(fs_output, mode, encoding=encoding)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 32.0.101.6127
OpenGL renderer: Intel(R) Iris(R) Xe Graphics
OpenGL vendor: Intel
Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: windows
Manufacturer: HP
Model: HP Elite x360 1040 14 inch G10 2-in-1 Notebook PC
OS: Microsoft Windows 11 Enterprise (Build 22631)
Memory: 16,794,263,552
MaxProcessMemory: 137,438,953,344
CPU: 12 13th Gen Intel(R) Core(TM) i7-1355U
OSLanguage: en-US
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2024.6.2
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
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: 2.2.4
ChimeraX-clix: 0.1.10
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: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
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-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
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: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
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: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
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: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
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: 1.4.1
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 24.1
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pywin32: 306
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
WMI: 1.5.1
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Seems unlikely that C:\path\ is correct. If this happens more often I might consider catching the error.