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Opened 5 hours ago
#19538 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: Linux-6.17.0-7-generic-x86_64-with-glibc2.42
ChimeraX Version: 1.11 (2025-12-17 06:45:39 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.11 (2025-12-17)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /home/k/MOR/GATI/results/vis_sessions/processed_aligned_chimera.cxs
> format session
Log from Tue Dec 23 19:33:37 2025 Startup Messages
---
warning | GBM is not supported with the current configuration. Fallback to Vulkan rendering in Chromium.
UCSF ChimeraX version: 1.11 (2025-12-17)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> cd /home/k/MOR/GATI
Current working directory is: /home/k/MOR/GATI
> open /home/k/MOR/GATI/data/processed_canonical/9PXV.pdb
> /home/k/MOR/GATI/data/processed_canonical/9PXW.pdb
> /home/k/MOR/GATI/data/processed_canonical/9PXX.pdb
> /home/k/MOR/GATI/data/processed_canonical/9PXY.pdb
> /home/k/MOR/GATI/data/processed_canonical/9PY2.pdb
> /home/k/MOR/GATI/data/processed_canonical/9PY3.pdb
> /home/k/MOR/GATI/data/processed_canonical/9PY4.pdb
Chain information for 9PXV.pdb #1
---
Chain | Description | UniProt
A | No description available | GNAI1_HUMAN 4-354
B | No description available | GBB1_MOUSE 6-340
C | No description available | GBG2_BOVIN 10-64
D | No description available | OPRM_HUMAN 67-352
Chain information for 9PXW.pdb #2
---
Chain | Description | UniProt
A | No description available | GNAI1_HUMAN 5-354
B | No description available | GBB1_MOUSE 4-340
C | No description available | GBG2_BOVIN 8-61
D | No description available | OPRM_HUMAN 68-354
Chain information for 9PXX.pdb #3
---
Chain | Description | UniProt
A | No description available | GNAI1_HUMAN 4-354
B | No description available | GBB1_MOUSE 6-340
C | No description available | GBG2_BOVIN 10-64
D | No description available | OPRM_HUMAN 67-352
Chain information for 9PXY.pdb #4
---
Chain | Description | UniProt
A | No description available | GNAI1_HUMAN 4-354
B | No description available | GBB1_MOUSE 6-340
C | No description available | GBG2_BOVIN 10-64
D | No description available | OPRM_HUMAN 67-352
Chain information for 9PY2.pdb #5
---
Chain | Description | UniProt
A | No description available | GNAI1_HUMAN 5-354
B | No description available | GBB1_MOUSE 4-340
C | No description available | GBG2_BOVIN 8-61
D | No description available | OPRM_HUMAN 67-352
Chain information for 9PY3.pdb #6
---
Chain | Description | UniProt
A | No description available | GNAI1_HUMAN 4-354
B | No description available | GBB1_MOUSE 6-340
C | No description available | GBG2_BOVIN 10-64
D | No description available | OPRM_HUMAN 67-352
Chain information for 9PY4.pdb #7
---
Chain | Description | UniProt
A | No description available | GNAI1_HUMAN 4-354
B | No description available | GBB1_MOUSE 6-340
C | No description available | GBG2_BOVIN 10-64
D | No description available | OPRM_HUMAN 67-352
Computing secondary structure
[Repeated 6 time(s)]
> ui tool show Matchmaker
> matchmaker #2,5#!3-4,6-7 to #1/D pairing bs
Parameters
---
Chain pairing | bs
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 9PXV.pdb, chain D (#1) with 9PXW.pdb, chain D (#2), sequence
alignment score = 1429.1
RMSD between 191 pruned atom pairs is 1.171 angstroms; (across all 285 pairs:
3.516)
Matchmaker 9PXV.pdb, chain D (#1) with 9PY2.pdb, chain D (#5), sequence
alignment score = 1469.2
RMSD between 285 pruned atom pairs is 0.615 angstroms; (across all 286 pairs:
0.626)
Matchmaker 9PXV.pdb, chain D (#1) with 9PXX.pdb, chain D (#3), sequence
alignment score = 1499.2
RMSD between 286 pruned atom pairs is 0.541 angstroms; (across all 286 pairs:
0.541)
Matchmaker 9PXV.pdb, chain D (#1) with 9PXY.pdb, chain D (#4), sequence
alignment score = 1508.8
RMSD between 286 pruned atom pairs is 0.512 angstroms; (across all 286 pairs:
0.512)
Matchmaker 9PXV.pdb, chain D (#1) with 9PY3.pdb, chain D (#6), sequence
alignment score = 1499.8
RMSD between 280 pruned atom pairs is 0.696 angstroms; (across all 286 pairs:
0.761)
Matchmaker 9PXV.pdb, chain D (#1) with 9PY4.pdb, chain D (#7), sequence
alignment score = 1490.2
RMSD between 284 pruned atom pairs is 0.628 angstroms; (across all 286 pairs:
0.650)
> save /home/k/MOR/GATI/results/vis_sessions/processed_aligned_chimera.cxs
> open /home/k/MOR/GATI/data/ski_full/MP_open.pdb
> /home/k/MOR/GATI/data/ski_full/MP_B2.pdb
> /home/k/MOR/GATI/data/ski_full/MP_B1.pdb
> /home/k/MOR/GATI/data/ski_full/MP_A.pdb
> /home/k/MOR/GATI/data/ski_full/LFT_open.pdb
> /home/k/MOR/GATI/data/ski_full/LFT_B2.pdb
> /home/k/MOR/GATI/data/ski_full/LFT_B1.pdb
> /home/k/MOR/GATI/data/ski_full/LFT_A.pdb
Summary of feedback from opening /home/k/MOR/GATI/data/ski_full/MP_open.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK GENERATED BY TRJCONV
Ignored bad PDB record found on line 3
REMARK THIS IS A SIMULATION BOX
Summary of feedback from opening /home/k/MOR/GATI/data/ski_full/MP_B2.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK GENERATED BY TRJCONV
Ignored bad PDB record found on line 3
REMARK THIS IS A SIMULATION BOX
Summary of feedback from opening /home/k/MOR/GATI/data/ski_full/MP_B1.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK GENERATED BY TRJCONV
Ignored bad PDB record found on line 3
REMARK THIS IS A SIMULATION BOX
Summary of feedback from opening /home/k/MOR/GATI/data/ski_full/MP_A.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK GENERATED BY TRJCONV
Ignored bad PDB record found on line 3
REMARK THIS IS A SIMULATION BOX
Summary of feedback from opening /home/k/MOR/GATI/data/ski_full/LFT_open.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK GENERATED BY TRJCONV
Ignored bad PDB record found on line 3
REMARK THIS IS A SIMULATION BOX
Summary of feedback from opening /home/k/MOR/GATI/data/ski_full/LFT_B2.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK GENERATED BY TRJCONV
Ignored bad PDB record found on line 3
REMARK THIS IS A SIMULATION BOX
Summary of feedback from opening /home/k/MOR/GATI/data/ski_full/LFT_B1.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK GENERATED BY TRJCONV
Ignored bad PDB record found on line 3
REMARK THIS IS A SIMULATION BOX
Summary of feedback from opening /home/k/MOR/GATI/data/ski_full/LFT_A.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK GENERATED BY TRJCONV
Ignored bad PDB record found on line 3
REMARK THIS IS A SIMULATION BOX
MP_open.pdb title:
Title [more info...]
Chain information for MP_open.pdb #8
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
Non-standard residues in MP_open.pdb #8
---
CYSG — (cysg)
CYSP — (cysp)
EIG — (EIG)
GLYM — (glym)
GTP — (GTP)
HSD — (HSD)
MG — (MG)
MP_B2.pdb title:
Title [more info...]
Chain information for MP_B2.pdb #9
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
Non-standard residues in MP_B2.pdb #9
---
CYSG — (cysg)
CYSP — (cysp)
EIG — (EIG)
GLYM — (glym)
GTP — (GTP)
HSD — (HSD)
MG — (MG)
MP_B1.pdb title:
Title [more info...]
Chain information for MP_B1.pdb #10
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
Non-standard residues in MP_B1.pdb #10
---
CYSG — (cysg)
CYSP — (cysp)
EIG — (EIG)
GLYM — (glym)
GTP — (GTP)
HSD — (HSD)
MG — (MG)
MP_A.pdb title:
Title [more info...]
Chain information for MP_A.pdb #11
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
Non-standard residues in MP_A.pdb #11
---
CYSG — (cysg)
CYSP — (cysp)
EIG — (EIG)
GLYM — (glym)
GTP — (GTP)
HSD — (HSD)
MG — (MG)
LFT_open.pdb title:
Title [more info...]
Chain information for LFT_open.pdb #12
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
Non-standard residues in LFT_open.pdb #12
---
CYSG — (cysg)
CYSP — (cysp)
EID — (EID)
GLYM — (glym)
GTP — (GTP)
HSD — (HSD)
MG — (MG)
LFT_B2.pdb title:
Title [more info...]
Chain information for LFT_B2.pdb #13
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
Non-standard residues in LFT_B2.pdb #13
---
CYSG — (cysg)
CYSP — (cysp)
EID — (EID)
GLYM — (glym)
GTP — (GTP)
HSD — (HSD)
MG — (MG)
LFT_B1.pdb title:
Title [more info...]
Chain information for LFT_B1.pdb #14
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
Non-standard residues in LFT_B1.pdb #14
---
CYSG — (cysg)
CYSP — (cysp)
EID — (EID)
GLYM — (glym)
GTP — (GTP)
HSD — (HSD)
MG — (MG)
LFT_A.pdb title:
Title [more info...]
Chain information for LFT_A.pdb #15
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
Non-standard residues in LFT_A.pdb #15
---
CYSG — (cysg)
CYSP — (cysp)
EID — (EID)
GLYM — (glym)
GTP — (GTP)
HSD — (HSD)
MG — (MG)
Computing secondary structure
[Repeated 7 time(s)]
> ui tool show Matchmaker
> matchmaker #2,5,8-15#!3-4,6-7 to #1/D pairing bs
Parameters
---
Chain pairing | bs
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 9PXV.pdb, chain D (#1) with 9PXW.pdb, chain D (#2), sequence
alignment score = 1429.1
RMSD between 191 pruned atom pairs is 1.171 angstroms; (across all 285 pairs:
3.516)
Matchmaker 9PXV.pdb, chain D (#1) with 9PY2.pdb, chain D (#5), sequence
alignment score = 1469.2
RMSD between 285 pruned atom pairs is 0.615 angstroms; (across all 286 pairs:
0.626)
Matchmaker 9PXV.pdb, chain D (#1) with MP_open.pdb, chain D (#8), sequence
alignment score = 1358.6
RMSD between 276 pruned atom pairs is 1.010 angstroms; (across all 286 pairs:
1.076)
Matchmaker 9PXV.pdb, chain D (#1) with MP_B2.pdb, chain D (#9), sequence
alignment score = 1436
RMSD between 204 pruned atom pairs is 1.082 angstroms; (across all 286 pairs:
3.332)
Matchmaker 9PXV.pdb, chain D (#1) with MP_B1.pdb, chain D (#10), sequence
alignment score = 1436
RMSD between 204 pruned atom pairs is 1.083 angstroms; (across all 286 pairs:
3.324)
Matchmaker 9PXV.pdb, chain D (#1) with MP_A.pdb, chain D (#11), sequence
alignment score = 1358.6
RMSD between 278 pruned atom pairs is 1.017 angstroms; (across all 286 pairs:
1.071)
Matchmaker 9PXV.pdb, chain D (#1) with LFT_open.pdb, chain D (#12), sequence
alignment score = 1370.6
RMSD between 280 pruned atom pairs is 0.963 angstroms; (across all 286 pairs:
1.001)
Matchmaker 9PXV.pdb, chain D (#1) with LFT_B2.pdb, chain D (#13), sequence
alignment score = 1436
RMSD between 204 pruned atom pairs is 1.081 angstroms; (across all 286 pairs:
3.327)
Matchmaker 9PXV.pdb, chain D (#1) with LFT_B1.pdb, chain D (#14), sequence
alignment score = 1413.8
RMSD between 165 pruned atom pairs is 1.102 angstroms; (across all 286 pairs:
3.577)
Matchmaker 9PXV.pdb, chain D (#1) with LFT_A.pdb, chain D (#15), sequence
alignment score = 1416.8
RMSD between 265 pruned atom pairs is 0.882 angstroms; (across all 286 pairs:
1.151)
Matchmaker 9PXV.pdb, chain D (#1) with 9PXX.pdb, chain D (#3), sequence
alignment score = 1499.2
RMSD between 286 pruned atom pairs is 0.541 angstroms; (across all 286 pairs:
0.541)
Matchmaker 9PXV.pdb, chain D (#1) with 9PXY.pdb, chain D (#4), sequence
alignment score = 1508.8
RMSD between 286 pruned atom pairs is 0.512 angstroms; (across all 286 pairs:
0.512)
Matchmaker 9PXV.pdb, chain D (#1) with 9PY3.pdb, chain D (#6), sequence
alignment score = 1499.8
RMSD between 280 pruned atom pairs is 0.696 angstroms; (across all 286 pairs:
0.761)
Matchmaker 9PXV.pdb, chain D (#1) with 9PY4.pdb, chain D (#7), sequence
alignment score = 1490.2
RMSD between 284 pruned atom pairs is 0.628 angstroms; (across all 286 pairs:
0.650)
> matchmaker #2,5,8-15#!3-4,6-7 to #1/D pairing bs
Parameters
---
Chain pairing | bs
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 9PXV.pdb, chain D (#1) with 9PXW.pdb, chain D (#2), sequence
alignment score = 1429.1
RMSD between 191 pruned atom pairs is 1.171 angstroms; (across all 285 pairs:
3.516)
Matchmaker 9PXV.pdb, chain D (#1) with 9PY2.pdb, chain D (#5), sequence
alignment score = 1469.2
RMSD between 285 pruned atom pairs is 0.615 angstroms; (across all 286 pairs:
0.626)
Matchmaker 9PXV.pdb, chain D (#1) with MP_open.pdb, chain D (#8), sequence
alignment score = 1358.6
RMSD between 276 pruned atom pairs is 1.010 angstroms; (across all 286 pairs:
1.076)
Matchmaker 9PXV.pdb, chain D (#1) with MP_B2.pdb, chain D (#9), sequence
alignment score = 1436
RMSD between 204 pruned atom pairs is 1.082 angstroms; (across all 286 pairs:
3.332)
Matchmaker 9PXV.pdb, chain D (#1) with MP_B1.pdb, chain D (#10), sequence
alignment score = 1436
RMSD between 204 pruned atom pairs is 1.083 angstroms; (across all 286 pairs:
3.324)
Matchmaker 9PXV.pdb, chain D (#1) with MP_A.pdb, chain D (#11), sequence
alignment score = 1358.6
RMSD between 278 pruned atom pairs is 1.017 angstroms; (across all 286 pairs:
1.071)
Matchmaker 9PXV.pdb, chain D (#1) with LFT_open.pdb, chain D (#12), sequence
alignment score = 1370.6
RMSD between 280 pruned atom pairs is 0.963 angstroms; (across all 286 pairs:
1.001)
Matchmaker 9PXV.pdb, chain D (#1) with LFT_B2.pdb, chain D (#13), sequence
alignment score = 1436
RMSD between 204 pruned atom pairs is 1.081 angstroms; (across all 286 pairs:
3.327)
Matchmaker 9PXV.pdb, chain D (#1) with LFT_B1.pdb, chain D (#14), sequence
alignment score = 1413.8
RMSD between 165 pruned atom pairs is 1.102 angstroms; (across all 286 pairs:
3.577)
Matchmaker 9PXV.pdb, chain D (#1) with LFT_A.pdb, chain D (#15), sequence
alignment score = 1416.8
RMSD between 265 pruned atom pairs is 0.882 angstroms; (across all 286 pairs:
1.151)
Matchmaker 9PXV.pdb, chain D (#1) with 9PXX.pdb, chain D (#3), sequence
alignment score = 1499.2
RMSD between 286 pruned atom pairs is 0.541 angstroms; (across all 286 pairs:
0.541)
Matchmaker 9PXV.pdb, chain D (#1) with 9PXY.pdb, chain D (#4), sequence
alignment score = 1508.8
RMSD between 286 pruned atom pairs is 0.512 angstroms; (across all 286 pairs:
0.512)
Matchmaker 9PXV.pdb, chain D (#1) with 9PY3.pdb, chain D (#6), sequence
alignment score = 1499.8
RMSD between 280 pruned atom pairs is 0.696 angstroms; (across all 286 pairs:
0.761)
Matchmaker 9PXV.pdb, chain D (#1) with 9PY4.pdb, chain D (#7), sequence
alignment score = 1490.2
RMSD between 284 pruned atom pairs is 0.628 angstroms; (across all 286 pairs:
0.650)
> save /home/k/MOR/GATI/results/vis_sessions/processed_aligned_chimera.cxs
——— End of log from Tue Dec 23 19:33:37 2025 ———
> view name session-start
opened ChimeraX session
> ui tool show "Show Sequence Viewer"
> hide target m
> show #5 models
> sequence chain #2/A #5/A
Alignment identifier is 1
> select add #11
16729 atoms, 16893 bonds, 1046 residues, 1 model selected
> select subtract #11
Nothing selected
> select
> #2/A:8-32,46-57,63-91,98-112,121-131,134-145,152-162,171-176,208-210,212-215,227-229,242-254,271-278,283-285,296-309,329-350
> #5/A:8-32,46-57,63-91,98-112,121-131,134-145,152-162,171-176,208-210,212-215,227-229,242-254,271-278,283-285,296-309,329-350
3094 atoms, 3100 bonds, 382 residues, 2 models selected
> sequence header rmsd setting initially_shown True
[Repeated 1 time(s)]
> save /home/k/MOR/GATI/results/vis_sessions/processed_aligned_chimera.cxs
> cd /home/k/MOR/GATI
Current working directory is: /home/k/MOR/GATI
> select #2/A:33-40,185-191,194-200,220-226,263-269,320-323
> #5/A:33-40,185-191,194-200,220-226,263-269,320-323
670 atoms, 680 bonds, 80 residues, 2 models selected
> select
> #2/A:8-32,46-57,63-91,98-112,121-131,134-145,152-162,171-176,208-210,212-215,227-229,242-254,271-278,283-285,296-309,329-350
> #5/A:8-32,46-57,63-91,98-112,121-131,134-145,152-162,171-176,208-210,212-215,227-229,242-254,271-278,283-285,296-309,329-350
3094 atoms, 3100 bonds, 382 residues, 2 models selected
> select #2/A:33-40,185-191,194-200,220-226,263-269,320-323
> #5/A:33-40,185-191,194-200,220-226,263-269,320-323
670 atoms, 680 bonds, 80 residues, 2 models selected
> select
> #2/A:8-32,46-57,63-91,98-112,121-131,134-145,152-162,171-176,208-210,212-215,227-229,242-254,271-278,283-285,296-309,329-350
> #5/A:8-32,46-57,63-91,98-112,121-131,134-145,152-162,171-176,208-210,212-215,227-229,242-254,271-278,283-285,296-309,329-350
3094 atoms, 3100 bonds, 382 residues, 2 models selected
> select #2/A:33-40,185-191,194-200,220-226,263-269,320-323
> #5/A:33-40,185-191,194-200,220-226,263-269,320-323
670 atoms, 680 bonds, 80 residues, 2 models selected
> select
> #2/A:8-32,46-57,63-91,98-112,121-131,134-145,152-162,171-176,208-210,212-215,227-229,242-254,271-278,283-285,296-309,329-350
> #5/A:8-32,46-57,63-91,98-112,121-131,134-145,152-162,171-176,208-210,212-215,227-229,242-254,271-278,283-285,296-309,329-350
3094 atoms, 3100 bonds, 382 residues, 2 models selected
No match chains chosen
> sequence match 1 #5/A to #2/A cutoffDistance 2.0
RMSD between 280 pruned atom pairs is 1.028 angstroms; (across all 350 pairs:
2.373)
> select #2/A:33-40,185-191,194-200,220-226,263-269,320-323
> #5/A:33-40,185-191,194-200,220-226,263-269,320-323
670 atoms, 680 bonds, 80 residues, 2 models selected
> sequence match 1 #5/A to #2/A cutoffDistance 2.0
RMSD between 280 pruned atom pairs is 1.028 angstroms; (across all 350 pairs:
2.373)
> show #11 models
> ui tool show "Model Panel"
> ui tool show "Task Manager"
> toolshed show
> ui tool show Matchmaker
> matchmaker #2,5,8-15#!3-4,6-7 to #1/D pairing bs
Parameters
---
Chain pairing | bs
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 9PXV.pdb, chain D (#1) with 9PXW.pdb, chain D (#2), sequence
alignment score = 1429.1
RMSD between 191 pruned atom pairs is 1.171 angstroms; (across all 285 pairs:
3.516)
Matchmaker 9PXV.pdb, chain D (#1) with 9PY2.pdb, chain D (#5), sequence
alignment score = 1469.2
RMSD between 285 pruned atom pairs is 0.615 angstroms; (across all 286 pairs:
0.626)
Matchmaker 9PXV.pdb, chain D (#1) with MP_open.pdb, chain D (#8), sequence
alignment score = 1358.6
RMSD between 276 pruned atom pairs is 1.010 angstroms; (across all 286 pairs:
1.076)
Matchmaker 9PXV.pdb, chain D (#1) with MP_B2.pdb, chain D (#9), sequence
alignment score = 1436
RMSD between 204 pruned atom pairs is 1.082 angstroms; (across all 286 pairs:
3.332)
Matchmaker 9PXV.pdb, chain D (#1) with MP_B1.pdb, chain D (#10), sequence
alignment score = 1436
RMSD between 204 pruned atom pairs is 1.083 angstroms; (across all 286 pairs:
3.324)
Matchmaker 9PXV.pdb, chain D (#1) with MP_A.pdb, chain D (#11), sequence
alignment score = 1358.6
RMSD between 278 pruned atom pairs is 1.017 angstroms; (across all 286 pairs:
1.071)
Matchmaker 9PXV.pdb, chain D (#1) with LFT_open.pdb, chain D (#12), sequence
alignment score = 1370.6
RMSD between 280 pruned atom pairs is 0.963 angstroms; (across all 286 pairs:
1.001)
Matchmaker 9PXV.pdb, chain D (#1) with LFT_B2.pdb, chain D (#13), sequence
alignment score = 1436
RMSD between 204 pruned atom pairs is 1.081 angstroms; (across all 286 pairs:
3.327)
Matchmaker 9PXV.pdb, chain D (#1) with LFT_B1.pdb, chain D (#14), sequence
alignment score = 1413.8
RMSD between 165 pruned atom pairs is 1.102 angstroms; (across all 286 pairs:
3.577)
Matchmaker 9PXV.pdb, chain D (#1) with LFT_A.pdb, chain D (#15), sequence
alignment score = 1416.8
RMSD between 265 pruned atom pairs is 0.882 angstroms; (across all 286 pairs:
1.151)
Matchmaker 9PXV.pdb, chain D (#1) with 9PXX.pdb, chain D (#3), sequence
alignment score = 1499.2
RMSD between 286 pruned atom pairs is 0.541 angstroms; (across all 286 pairs:
0.541)
Matchmaker 9PXV.pdb, chain D (#1) with 9PXY.pdb, chain D (#4), sequence
alignment score = 1508.8
RMSD between 286 pruned atom pairs is 0.512 angstroms; (across all 286 pairs:
0.512)
Matchmaker 9PXV.pdb, chain D (#1) with 9PY3.pdb, chain D (#6), sequence
alignment score = 1499.8
RMSD between 280 pruned atom pairs is 0.696 angstroms; (across all 286 pairs:
0.761)
Matchmaker 9PXV.pdb, chain D (#1) with 9PY4.pdb, chain D (#7), sequence
alignment score = 1490.2
RMSD between 284 pruned atom pairs is 0.628 angstroms; (across all 286 pairs:
0.650)
> matchmaker #2,5,8-15#!3-4,6-7 to #1/D pairing bs
Parameters
---
Chain pairing | bs
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 9PXV.pdb, chain D (#1) with 9PXW.pdb, chain D (#2), sequence
alignment score = 1429.1
RMSD between 191 pruned atom pairs is 1.171 angstroms; (across all 285 pairs:
3.516)
Matchmaker 9PXV.pdb, chain D (#1) with 9PY2.pdb, chain D (#5), sequence
alignment score = 1469.2
RMSD between 285 pruned atom pairs is 0.615 angstroms; (across all 286 pairs:
0.626)
Matchmaker 9PXV.pdb, chain D (#1) with MP_open.pdb, chain D (#8), sequence
alignment score = 1358.6
RMSD between 276 pruned atom pairs is 1.010 angstroms; (across all 286 pairs:
1.076)
Matchmaker 9PXV.pdb, chain D (#1) with MP_B2.pdb, chain D (#9), sequence
alignment score = 1436
RMSD between 204 pruned atom pairs is 1.082 angstroms; (across all 286 pairs:
3.332)
Matchmaker 9PXV.pdb, chain D (#1) with MP_B1.pdb, chain D (#10), sequence
alignment score = 1436
RMSD between 204 pruned atom pairs is 1.083 angstroms; (across all 286 pairs:
3.324)
Matchmaker 9PXV.pdb, chain D (#1) with MP_A.pdb, chain D (#11), sequence
alignment score = 1358.6
RMSD between 278 pruned atom pairs is 1.017 angstroms; (across all 286 pairs:
1.071)
Matchmaker 9PXV.pdb, chain D (#1) with LFT_open.pdb, chain D (#12), sequence
alignment score = 1370.6
RMSD between 280 pruned atom pairs is 0.963 angstroms; (across all 286 pairs:
1.001)
Matchmaker 9PXV.pdb, chain D (#1) with LFT_B2.pdb, chain D (#13), sequence
alignment score = 1436
RMSD between 204 pruned atom pairs is 1.081 angstroms; (across all 286 pairs:
3.327)
Matchmaker 9PXV.pdb, chain D (#1) with LFT_B1.pdb, chain D (#14), sequence
alignment score = 1413.8
RMSD between 165 pruned atom pairs is 1.102 angstroms; (across all 286 pairs:
3.577)
Matchmaker 9PXV.pdb, chain D (#1) with LFT_A.pdb, chain D (#15), sequence
alignment score = 1416.8
RMSD between 265 pruned atom pairs is 0.882 angstroms; (across all 286 pairs:
1.151)
Matchmaker 9PXV.pdb, chain D (#1) with 9PXX.pdb, chain D (#3), sequence
alignment score = 1499.2
RMSD between 286 pruned atom pairs is 0.541 angstroms; (across all 286 pairs:
0.541)
Matchmaker 9PXV.pdb, chain D (#1) with 9PXY.pdb, chain D (#4), sequence
alignment score = 1508.8
RMSD between 286 pruned atom pairs is 0.512 angstroms; (across all 286 pairs:
0.512)
Matchmaker 9PXV.pdb, chain D (#1) with 9PY3.pdb, chain D (#6), sequence
alignment score = 1499.8
RMSD between 280 pruned atom pairs is 0.696 angstroms; (across all 286 pairs:
0.761)
Matchmaker 9PXV.pdb, chain D (#1) with 9PY4.pdb, chain D (#7), sequence
alignment score = 1490.2
RMSD between 284 pruned atom pairs is 0.628 angstroms; (across all 286 pairs:
0.650)
> ui tool show "Similar Structures"
You must press the similar structures Search button before you can open
matching structures.
[Repeated 1 time(s)]Must choose a chain in the similar structures panel before
running search
> foldseek #6/A
Not saving entity_poly_seq for non-authoritative sequences
> foldseek #6/A
Foldseek search in progress. Cannot run another search until current one
completes.
Found 918 similar structures to 9PY3.pdb #6/A in pdb database using foldseek,
name fs1
> ui tool show "Modeller Comparative"
> sequence disassociate #5/A
Disassociated 9PY2.pdb chain A from 2 chains
> sequence associate #1/D
Associated 9PXV.pdb chain D to 2 chains with 275 mismatches and/or gaps
> sequence disassociate #2/A
Disassociated 9PXW.pdb chain A from 2 chains
> sequence disassociate #1/D
Disassociated 9PXV.pdb chain D from 2 chains
> sequence associate #2/A
Associated 9PXW.pdb chain A to 2 chains with 0 mismatches
> sequence disassociate #2/A
Disassociated 9PXW.pdb chain A from 2 chains
> sequence associate #9/A
Associated MP_B2.pdb chain A to 2 chains with 6 mismatches
> sequence disassociate #9/A
Disassociated MP_B2.pdb chain A from 2 chains
> sequence associate #11/A
Associated MP_A.pdb chain A to 2 chains with 6 mismatches
> ui tool show "Modeller Comparative"
> modeller comparative 1:1 numModels 5 fast false multichain true hetPreserve
> false hydrogens false waterPreserve false executableLocation
> /usr/bin/mod10.8
Modeller output
MODELLER 10.8, 2025/11/04, r13157
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2025 Andrej Sali
All Rights Reserved
Written by A. Sali
with help from
B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong,
M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva,
A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov,
F. Melo, J.P. Overington, E. Feyfant
University of California, San Francisco, USA
Rockefeller University, New York, USA
Harvard University, Cambridge, USA
Imperial Cancer Research Fund, London, UK
Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, Linux fl1509 6.17.0-7-generic x86_64
Date and time of compilation : 2025/11/04 18:30:22
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2025/12/24 13:17:57
environ____W> The class 'environ' is deprecated; use 'Environ' instead
openf___224_> Open $(LIB)/restyp.lib
openf___224_> Open ${MODINSTALL10v8}/modlib/restyp_cif.lib
openf___224_> Open ${MODINSTALL10v8}/modlib/resgrp.lib
rdresgr_266_> Number of residue groups: 2
openf___224_> Open ${MODINSTALL10v8}/modlib/sstruc.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 194446 189.889 0.185
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 194974 190.404 0.186
openf___224_> Open ${MODINSTALL10v8}/modlib/resdih.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 243574 237.865 0.232
rdrdih__263_> Number of dihedral angle types : 9
Maximal number of dihedral angle optima: 3
Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5
openf___224_> Open ${MODINSTALL10v8}/modlib/radii.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 256874 250.854 0.245
openf___224_> Open ${MODINSTALL10v8}/modlib/af_mnchdef.lib
rdwilmo_274_> Mainchain residue conformation classes: APBLE
openf___224_> Open ${MODINSTALL10v8}/modlib/mnch.lib
rdclass_257_> Number of classes: 5
openf___224_> Open ${MODINSTALL10v8}/modlib/mnch1.lib
openf___224_> Open ${MODINSTALL10v8}/modlib/mnch2.lib
openf___224_> Open ${MODINSTALL10v8}/modlib/mnch3.lib
openf___224_> Open ${MODINSTALL10v8}/modlib/xs4.mat
rdrrwgh_268_> Number of residue types: 21
automodel__W> The class 'automodel' is deprecated; use 'AutoModel' instead
openf___224_> Open alignment.ali
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 285569 278.876 0.272
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 300661 293.614 0.287
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 316061 308.653 0.301
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 346861 338.731 0.331
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 408461 398.888 0.390
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 531661 519.200 0.507
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 778061 759.825 0.742
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 778089 759.853 0.742
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 778117 759.880 0.742
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 778145 759.907 0.742
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 778173 759.935 0.742
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 782341 764.005 0.746
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 783737 765.368 0.747
read_al_374_> Non-standard residue type,position,sequence: X 1 1
read_al_374_> Non-standard residue type,position,sequence: X 2 1
read_al_374_> Non-standard residue type,position,sequence: . 56 1
read_al_374_> Non-standard residue type,position,sequence: . 187 1
read_al_374_> Non-standard residue type,position,sequence: . 194 1
read_al_374_> Non-standard residue type,position,sequence: . 212 1
read_al_374_> Non-standard residue type,position,sequence: . 243 1
read_al_374_> Non-standard residue type,position,sequence: . 321 1
read_al_374_> Non-standard residue type,position,sequence: X 406 1
read_al_374_> Non-standard residue type,position,sequence: X 414 1
read_al_374_> Non-standard residue type,position,sequence: X 443 1
read_al_374_> Non-standard residue type,position,sequence: X 494 1
read_al_374_> Non-standard residue type,position,sequence: X 535 1
read_al_374_> Non-standard residue type,position,sequence: X 577 1
read_al_374_> Non-standard residue type,position,sequence: X 618 1
read_al_374_> Non-standard residue type,position,sequence: X 663 1
read_al_374_> Non-standard residue type,position,sequence: X 730 1
read_al_374_> Non-standard residue type,position,sequence: X 754 1
read_al_374_> Non-standard residue type,position,sequence: X 862 1
read_al_374_> Non-standard residue type,position,sequence: X 914 1
read_al_374_> Non-standard residue type,position,sequence: X 988 1
read_al_374_> Non-standard residue type,position,sequence: X 1010 1
Read the alignment from file : alignment.ali
Total number of alignment positions: 1043
# Code #_Res #_Segm PDB_code Name
-------------------------------------------------------------------------------
1 MP_A.pdb_ 1043 4 MP_A.pdb_11
2 2_chains 350 1 2_chains
check_a_343_> >> BEGINNING OF COMMAND
openf___224_> Open ./template_struc/MP_A.pdb_11.pdb
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1098362 1072.619 1.047
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1098362 1072.619 1.047
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1098533 1072.786 1.048
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1099383 1073.616 1.048
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1100641 1074.845 1.050
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1102545 1076.704 1.051
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1102545 1076.704 1.051
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1102635 1076.792 1.052
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1105491 1079.581 1.054
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1105491 1079.581 1.054
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1105626 1079.713 1.054
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1109910 1083.896 1.058
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1109910 1083.896 1.058
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1110108 1084.090 1.059
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1116534 1090.365 1.065
read_pd_459W> Residue type HSD not recognized. 'AutoModel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1116534 1090.365 1.065
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1116831 1090.655 1.065
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1126453 1100.052 1.074
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1126453 1100.052 1.074
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1126903 1100.491 1.075
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1141353 1114.603 1.088
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1141353 1114.603 1.088
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1142028 1115.262 1.089
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1163686 1136.412 1.110
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1163686 1136.412 1.110
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1164694 1137.396 1.111
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1197198 1169.139 1.142
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1197198 1169.139 1.142
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1198710 1170.615 1.143
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1198710 1170.615 1.143
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1198710 1170.615 1.143
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1247466 1218.229 1.190
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1247466 1218.229 1.190
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1249734 1220.443 1.192
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1322868 1291.863 1.262
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1322868 1291.863 1.262
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1326270 1295.186 1.265
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1435954 1402.299 1.369
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1435126 1401.490 1.369
read_te_291E> Sequence difference between alignment and pdb :
x (mismatch at alignment position 1)
Alignment XXTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKII
PDB TLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKII.E
Match ** *
Alignment residue type 24 (X, UNK) does not match pdb
residue type 17 (T, THR),
for align code MP_A.pdb_11 (atom file MP_A.pdb_11), pdb residue number " 4", chain "A"
Please check your alignment file header to be sure you correctly specified
the starting and ending residue numbers and chains. The alignment sequence
must match that from the atom file exactly.
Another possibility is that some residues in the atom file are missing,
perhaps because they could not be resolved experimentally. (Note that Modeller
reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.)
In this case, simply replace the section of your alignment corresponding
to these missing residues with gaps.
read_te_288W> Protein not accepted: 1 MP_A.pdb_11
Modeller errors
Could not find platform independent libraries
Could not find platform dependent libraries
Consider setting $PYTHONHOME to [:]
'import site' failed; use -v for traceback
Traceback (most recent call last):
File "/tmp/tmpzfn5aqeu/ModellerModelling.py", line 88, in ?
a.make()
File "/usr/lib/modeller10.8/modlib/modeller/automodel/automodel.py", line 143, in make
self.homcsr(exit_stage)
File "/usr/lib/modeller10.8/modlib/modeller/automodel/automodel.py", line 655, in homcsr
self.check_alignment(aln)
File "/usr/lib/modeller10.8/modlib/modeller/automodel/automodel.py", line 601, in check_alignment
aln.check()
File "/usr/lib/modeller10.8/modlib/modeller/alignment.py", line 215, in check
self.check_structure_structure(io=io)
File "/usr/lib/modeller10.8/modlib/modeller/alignment.py", line 224, in check_structure_structure
return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst)
_modeller.SequenceMismatchError: read_te_291E> Sequence difference between alignment and pdb :
Exception in thread Thread-152 (threaded_run):
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/modeller/common.py", line 750, in threaded_run
_ = subprocess.run(cmd, capture_output=True, text=True, check=True,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/subprocess.py", line 571, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['/usr/bin/mod10.8',
'/tmp/tmpzfn5aqeu/ModellerModelling.py']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1045, in
_bootstrap_inner
self.run()
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 982, in run
self._target(*self._args, **self._kwargs)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/modeller/common.py", line 762, in threaded_run
raise UserError("Modeller execution failed; output and errors in log")
chimerax.core.errors.UserError: Modeller execution failed; output and errors
in log
> ui tool show "Task Manager"
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 919, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 936, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/taskmanager/tool.py", line 101, in <lambda>
self.table.add_column("Runtime", data_fetch=lambda x:
self._get_runtime(x.runtime))
^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 919, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 936, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/taskmanager/tool.py", line 101, in <lambda>
self.table.add_column("Runtime", data_fetch=lambda x:
self._get_runtime(x.runtime))
^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 919, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 936, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/taskmanager/tool.py", line 101, in <lambda>
self.table.add_column("Runtime", data_fetch=lambda x:
self._get_runtime(x.runtime))
^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 919, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 936, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/taskmanager/tool.py", line 101, in <lambda>
self.table.add_column("Runtime", data_fetch=lambda x:
self._get_runtime(x.runtime))
^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 919, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 936, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/taskmanager/tool.py", line 101, in <lambda>
self.table.add_column("Runtime", data_fetch=lambda x:
self._get_runtime(x.runtime))
^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 919, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 936, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/taskmanager/tool.py", line 101, in <lambda>
self.table.add_column("Runtime", data_fetch=lambda x:
self._get_runtime(x.runtime))
^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 919, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 936, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/taskmanager/tool.py", line 101, in <lambda>
self.table.add_column("Runtime", data_fetch=lambda x:
self._get_runtime(x.runtime))
^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 919, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 936, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/taskmanager/tool.py", line 101, in <lambda>
self.table.add_column("Runtime", data_fetch=lambda x:
self._get_runtime(x.runtime))
^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 919, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 936, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/taskmanager/tool.py", line 101, in <lambda>
self.table.add_column("Runtime", data_fetch=lambda x:
self._get_runtime(x.runtime))
^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 919, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 936, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/taskmanager/tool.py", line 101, in <lambda>
self.table.add_column("Runtime", data_fetch=lambda x:
self._get_runtime(x.runtime))
^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 919, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 936, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/taskmanager/tool.py", line 101, in <lambda>
self.table.add_column("Runtime", data_fetch=lambda x:
self._get_runtime(x.runtime))
^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 919, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 936, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/taskmanager/tool.py", line 101, in <lambda>
self.table.add_column("Runtime", data_fetch=lambda x:
self._get_runtime(x.runtime))
^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 919, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 936, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/taskmanager/tool.py", line 101, in <lambda>
self.table.add_column("Runtime", data_fetch=lambda x:
self._get_runtime(x.runtime))
^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 919, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 936, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/taskmanager/tool.py", line 101, in <lambda>
self.table.add_column("Runtime", data_fetch=lambda x:
self._get_runtime(x.runtime))
^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 919, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 936, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/taskmanager/tool.py", line 101, in <lambda>
self.table.add_column("Runtime", data_fetch=lambda x:
self._get_runtime(x.runtime))
^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 919, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 936, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/taskmanager/tool.py", line 101, in <lambda>
self.table.add_column("Runtime", data_fetch=lambda x:
self._get_runtime(x.runtime))
^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 919, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 936, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/taskmanager/tool.py", line 101, in <lambda>
self.table.add_column("Runtime", data_fetch=lambda x:
self._get_runtime(x.runtime))
^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 919, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 936, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/taskmanager/tool.py", line 101, in <lambda>
self.table.add_column("Runtime", data_fetch=lambda x:
self._get_runtime(x.runtime))
^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 919, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 936, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/taskmanager/tool.py", line 101, in <lambda>
self.table.add_column("Runtime", data_fetch=lambda x:
self._get_runtime(x.runtime))
^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 919, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 936, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/taskmanager/tool.py", line 101, in <lambda>
self.table.add_column("Runtime", data_fetch=lambda x:
self._get_runtime(x.runtime))
^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 919, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 936, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/taskmanager/tool.py", line 101, in <lambda>
self.table.add_column("Runtime", data_fetch=lambda x:
self._get_runtime(x.runtime))
^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 919, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 936, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/taskmanager/tool.py", line 101, in <lambda>
self.table.add_column("Runtime", data_fetch=lambda x:
self._get_runtime(x.runtime))
^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 919, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 936, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/taskmanager/tool.py", line 101, in <lambda>
self.table.add_column("Runtime", data_fetch=lambda x:
self._get_runtime(x.runtime))
^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 919, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 936, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/taskmanager/tool.py", line 101, in <lambda>
self.table.add_column("Runtime", data_fetch=lambda x:
self._get_runtime(x.runtime))
^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 919, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 936, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/taskmanager/tool.py", line 101, in <lambda>
self.table.add_column("Runtime", data_fetch=lambda x:
self._get_runtime(x.runtime))
^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 919, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 936, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/taskmanager/tool.py", line 101, in <lambda>
self.table.add_column("Runtime", data_fetch=lambda x:
self._get_runtime(x.runtime))
^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 919, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 936, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/taskmanager/tool.py", line 101, in <lambda>
self.table.add_column("Runtime", data_fetch=lambda x:
self._get_runtime(x.runtime))
^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 919, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 936, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/taskmanager/tool.py", line 101, in <lambda>
self.table.add_column("Runtime", data_fetch=lambda x:
self._get_runtime(x.runtime))
^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 919, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 936, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/taskmanager/tool.py", line 101, in <lambda>
self.table.add_column("Runtime", data_fetch=lambda x:
self._get_runtime(x.runtime))
^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 919, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 936, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/taskmanager/tool.py", line 101, in <lambda>
self.table.add_column("Runtime", data_fetch=lambda x:
self._get_runtime(x.runtime))
^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 919, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 936, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/taskmanager/tool.py", line 101, in <lambda>
self.table.add_column("Runtime", data_fetch=lambda x:
self._get_runtime(x.runtime))
^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 919, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 936, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/taskmanager/tool.py", line 101, in <lambda>
self.table.add_column("Runtime", data_fetch=lambda x:
self._get_runtime(x.runtime))
^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 919, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 936, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/taskmanager/tool.py", line 101, in <lambda>
self.table.add_column("Runtime", data_fetch=lambda x:
self._get_runtime(x.runtime))
^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 919, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 936, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/taskmanager/tool.py", line 101, in <lambda>
self.table.add_column("Runtime", data_fetch=lambda x:
self._get_runtime(x.runtime))
^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
TypeError: unsupported operand type(s) for -: 'NoneType' and
'datetime.datetime'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 186, in runtime
return self.end_time - self.start_time
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 580.95.05
OpenGL renderer: NVIDIA RTX A4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.13
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: xcb
XDG_SESSION_TYPE=wayland
DESKTOP_SESSION=
XDG_SESSION_DESKTOP=
XDG_CURRENT_DESKTOP=niri
DISPLAY=:0
WAYLAND_DISPLAY=wayland-1
Manufacturer: Dell Inc.
Model: Precision 5820 Tower
OS: Ubuntu 25.10
Architecture: 64bit ELF
Virtual Machine: none
CPU: 20 Intel(R) Xeon(R) W-2255 CPU @ 3.70GHz
Cache Size: 19712 KB
Memory:
total used free shared buff/cache available
Mem: 251Gi 58Gi 21Gi 1.6Gi 156Gi 193Gi
Swap: 2.0Gi 0B 2.0Gi
Graphics:
0000:b3:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA104GL [RTX A4000] [10de:24b0] (rev a1)
Subsystem: Dell Device [1028:14ad]
Kernel driver in use: nvidia
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.0
appdirs: 1.4.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
biopython: 1.83
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2025.11.12
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-clix: 0.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMalign: 0.1.3
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: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.2.2
ChimeraX-locscalesurfer: 0.1.1
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
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: 1.0.1
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: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.11
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-QScore: 1.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
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: 1.19.1
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: 2.5.2
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: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
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: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
DiffFit: 0.7.0
distro: 1.9.0
docutils: 0.21.2
einops: 0.3.2
executing: 2.2.1
filelock: 3.19.1
finufft: 2.4.1
fonttools: 4.61.1
frozenlist: 1.8.0
fsspec: 2025.12.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.25.1
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
mpmath: 1.3.0
mrcfile: 1.3.0
msgpack: 1.1.1
multidict: 6.7.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.24.4
numpy: 1.26.4
nvidia-cublas-cu12: 12.1.3.1
nvidia-cuda-cupti-cu12: 12.1.105
nvidia-cuda-nvrtc-cu12: 12.1.105
nvidia-cuda-runtime-cu12: 12.1.105
nvidia-cudnn-cu12: 8.9.2.26
nvidia-cufft-cu12: 11.0.2.54
nvidia-curand-cu12: 10.3.2.106
nvidia-cusolver-cu12: 11.4.5.107
nvidia-cusparse-cu12: 12.1.0.106
nvidia-nccl-cu12: 2.19.3
nvidia-nvjitlink-cu12: 12.9.86
nvidia-nvtx-cu12: 12.1.105
OpenMM: 8.2.0
OpenMM-CUDA-12: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.1
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.2.5
pyproject_hooks: 1.2.0
PyQt6: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pytz: 2025.2
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.0.0
roman-numerals-py: 4.0.0
rpds-py: 0.30.0
scipy: 1.10.1
scipy: 1.14.0
Send2Trash: 1.8.3
SEQCROW: 1.9.4
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
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
sse-starlette: 3.0.4
stack-data: 0.6.3
starlette: 0.50.0
superqt: 0.7.6
sympy: 1.14.0
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
timm: 0.4.12
tinyarray: 1.2.5
torch: 2.2.2
torchvision: 0.17.2
tornado: 6.5.4
tqdm: 4.66.6
traitlets: 5.14.3
triton: 2.2.0
typing-inspection: 0.4.2
typing_extensions: 4.15.0
tzdata: 2025.3
urllib3: 2.6.2
uvicorn: 0.38.0
wcwidth: 0.2.14
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
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