![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 15 hours ago
#19529 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: macOS-26.2-arm64-arm-64bit
ChimeraX Version: 1.11 (2025-12-17 06:45:39 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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{
"uptime" : 40000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac15,10",
"coalitionID" : 36496,
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"build" : "25C56",
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"captureTime" : "2025-12-20 13:33:17.5079 -0500",
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"incident" : "9B6D859A-B18D-42F4-A781-34322652A3BA",
"pid" : 33148,
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"procLaunch" : "2025-12-20 13:29:34.5877 -0500",
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"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "0C182869-1922-DD4F-7F6A-EE8F5CB6EFA9",
"appleIntelligenceStatus" : {"state":"available"},
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"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
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"vmRegionInfo" : "0x8 is not in any region. Bytes before following region: 4371939320
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
__TEXT 104968000-10496c000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.11.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000008","rawCodes":[1,8],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000008"},
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"vmregioninfo" : "0x8 is not in any region. Bytes before following region: 4371939320
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
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Log:
UCSF ChimeraX version: 1.11 (2025-12-17)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/lynnehowell/SickKids Research Dropbox/Howell Lab's shared
> workspace/Grants/CIHR 2026 PNAG-alginate/Alginate Section/Alginate
> models.cxs"
Log from Sat Dec 20 13:53:51 2025UCSF ChimeraX version: 1.11 (2025-12-17)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/lynnehowell/SickKids Research Dropbox/Howell Lab's shared
> workspace/Grants/CIHR 2026 PNAG-alginate/Alginate Section/Alginate
> models.cxs"
Log from Fri Dec 19 16:32:43 2025UCSF ChimeraX version: 1.11 (2025-12-17)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/lynne/SickKids Research Dropbox/Howell Lab's shared
> workspace/Grants/CIHR 2026 PNAG-alginate/Alginate Section/Alginate
> models.cxs" format session
Log from Thu Dec 18 15:12:06 2025UCSF ChimeraX version: 1.11 (2025-12-17)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/lynne/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3
> predictions/Alginate/fold_alg844/fold_alg844_model_0.cif"
Chain information for fold_alg844_model_0.cif #1
---
Chain | Description
A | .
B | .
Computing secondary structure
> open "/Users/lynne/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3
> predictions/Alginate/fold_alg844/fold_alg844_model_1.cif"
Chain information for fold_alg844_model_1.cif #2
---
Chain | Description
A | .
B | .
> open "/Users/lynne/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3
> predictions/Alginate/fold_alg844/fold_alg844_model_2.cif"
Chain information for fold_alg844_model_2.cif #3
---
Chain | Description
A | .
B | .
> open "/Users/lynne/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3
> predictions/Alginate/fold_alg844/fold_alg844_model_3.cif"
Chain information for fold_alg844_model_3.cif #4
---
Chain | Description
A | .
B | .
> open "/Users/lynne/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3
> predictions/Alginate/fold_alg844/fold_alg844_model_4.cif"
Chain information for fold_alg844_model_4.cif #5
---
Chain | Description
A | .
B | .
Computing secondary structure
[Repeated 3 time(s)]
> ui tool show Matchmaker
> matchmaker #2-5 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_alg844_model_0.cif, chain A (#1) with fold_alg844_model_1.cif,
chain A (#2), sequence alignment score = 2607.3
RMSD between 494 pruned atom pairs is 0.330 angstroms; (across all 494 pairs:
0.330)
Matchmaker fold_alg844_model_0.cif, chain A (#1) with fold_alg844_model_2.cif,
chain A (#3), sequence alignment score = 2607.9
RMSD between 480 pruned atom pairs is 0.395 angstroms; (across all 494 pairs:
1.285)
Matchmaker fold_alg844_model_0.cif, chain A (#1) with fold_alg844_model_3.cif,
chain A (#4), sequence alignment score = 2610.9
RMSD between 494 pruned atom pairs is 0.414 angstroms; (across all 494 pairs:
0.414)
Matchmaker fold_alg844_model_0.cif, chain A (#1) with fold_alg844_model_4.cif,
chain A (#5), sequence alignment score = 2607.9
RMSD between 480 pruned atom pairs is 0.482 angstroms; (across all 494 pairs:
1.301)
> open "/Users/lynne/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3
> predictions/Alginate/fold_alg844_dimer_g/fold_alg844_dimer_g_model_0.cif"
Chain information for fold_alg844_dimer_g_model_0.cif #6
---
Chain | Description
A | .
B C | .
D | .
> open "/Users/lynne/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3
> predictions/Alginate/fold_alg844_dimer_g/fold_alg844_dimer_g_model_1.cif"
Chain information for fold_alg844_dimer_g_model_1.cif #7
---
Chain | Description
A | .
B C | .
D | .
> open "/Users/lynne/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3
> predictions/Alginate/fold_alg844_dimer_g/fold_alg844_dimer_g_model_2.cif"
Chain information for fold_alg844_dimer_g_model_2.cif #8
---
Chain | Description
A | .
B C | .
D | .
> open "/Users/lynne/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3
> predictions/Alginate/fold_alg844_dimer_g/fold_alg844_dimer_g_model_3.cif"
Chain information for fold_alg844_dimer_g_model_3.cif #9
---
Chain | Description
A | .
B C | .
D | .
> open "/Users/lynne/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3
> predictions/Alginate/fold_alg844_dimer_g/fold_alg844_dimer_g_model_4.cif"
Chain information for fold_alg844_dimer_g_model_4.cif #10
---
Chain | Description
A | .
B C | .
D | .
Computing secondary structure
[Repeated 4 time(s)]
> delete #6
> delete #7
> delete #8
> delete #9
> delete #10
> open "/Users/lynne/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3
> predictions/Alginate/fold_alg844kxijf/fold_alg844kxijf_model_0.cif"
Chain information for fold_alg844kxijf_model_0.cif #6
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
G | .
> open "/Users/lynne/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3
> predictions/Alginate/fold_alg844kxijf/fold_alg844kxijf_model_1.cif"
Chain information for fold_alg844kxijf_model_1.cif #7
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
G | .
> open "/Users/lynne/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3
> predictions/Alginate/fold_alg844kxijf/fold_alg844kxijf_model_2.cif"
Chain information for fold_alg844kxijf_model_2.cif #8
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
G | .
> open "/Users/lynne/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3
> predictions/Alginate/fold_alg844kxijf/fold_alg844kxijf_model_3.cif"
Chain information for fold_alg844kxijf_model_3.cif #9
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
G | .
> open "/Users/lynne/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3
> predictions/Alginate/fold_alg844kxijf/fold_alg844kxijf_model_4.cif"
Chain information for fold_alg844kxijf_model_4.cif #10
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
G | .
> hide atoms
> show cartoons
Computing secondary structure
[Repeated 4 time(s)]
> ui tool show Matchmaker
> matchmaker #6-10 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_alg844_model_0.cif, chain A (#1) with
fold_alg844kxijf_model_0.cif, chain A (#6), sequence alignment score = 2602.5
RMSD between 477 pruned atom pairs is 0.798 angstroms; (across all 494 pairs:
1.170)
Matchmaker fold_alg844_model_0.cif, chain A (#1) with
fold_alg844kxijf_model_1.cif, chain A (#7), sequence alignment score = 2598.9
RMSD between 464 pruned atom pairs is 0.769 angstroms; (across all 494 pairs:
1.167)
Matchmaker fold_alg844_model_0.cif, chain A (#1) with
fold_alg844kxijf_model_2.cif, chain A (#8), sequence alignment score = 2602.5
RMSD between 454 pruned atom pairs is 0.825 angstroms; (across all 494 pairs:
1.324)
Matchmaker fold_alg844_model_0.cif, chain A (#1) with
fold_alg844kxijf_model_3.cif, chain A (#9), sequence alignment score = 2598.9
RMSD between 463 pruned atom pairs is 0.889 angstroms; (across all 494 pairs:
1.319)
Matchmaker fold_alg844_model_0.cif, chain A (#1) with
fold_alg844kxijf_model_4.cif, chain A (#10), sequence alignment score = 2602.5
RMSD between 475 pruned atom pairs is 0.771 angstroms; (across all 494 pairs:
1.188)
> open "/Users/lynne/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3
> predictions/Alginate/fold_algkxijf/fold_algkxijf_model_0.cif"
Chain information for fold_algkxijf_model_0.cif #11
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
> open "/Users/lynne/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3
> predictions/Alginate/fold_algkxijf/fold_algkxijf_model_1.cif"
Chain information for fold_algkxijf_model_1.cif #12
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
> open "/Users/lynne/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3
> predictions/Alginate/fold_algkxijf/fold_algkxijf_model_2.cif"
Chain information for fold_algkxijf_model_2.cif #13
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
> open "/Users/lynne/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3
> predictions/Alginate/fold_algkxijf/fold_algkxijf_model_3.cif"
Chain information for fold_algkxijf_model_3.cif #14
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
> open "/Users/lynne/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3
> predictions/Alginate/fold_algkxijf/fold_algkxijf_model_4.cif"
Chain information for fold_algkxijf_model_4.cif #15
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
> hide atoms
> ui tool show Matchmaker
> matchmaker #12-15 to #11
Computing secondary structure
[Repeated 4 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_algkxijf_model_0.cif, chain C (#11) with
fold_algkxijf_model_1.cif, chain C (#12), sequence alignment score = 2723.2
RMSD between 473 pruned atom pairs is 0.361 angstroms; (across all 520 pairs:
3.605)
Matchmaker fold_algkxijf_model_0.cif, chain C (#11) with
fold_algkxijf_model_2.cif, chain C (#13), sequence alignment score = 2740.6
RMSD between 490 pruned atom pairs is 0.411 angstroms; (across all 520 pairs:
3.001)
Matchmaker fold_algkxijf_model_0.cif, chain C (#11) with
fold_algkxijf_model_3.cif, chain C (#14), sequence alignment score = 2737.6
RMSD between 476 pruned atom pairs is 0.416 angstroms; (across all 520 pairs:
3.810)
Matchmaker fold_algkxijf_model_0.cif, chain C (#11) with
fold_algkxijf_model_4.cif, chain C (#15), sequence alignment score = 2719
RMSD between 470 pruned atom pairs is 0.398 angstroms; (across all 520 pairs:
4.424)
> hide #1 models
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> hide #6 models
> hide #7 models
> hide #8 models
> hide #9 models
> hide #10 models
> show #11-15 cartoons
> open "/Users/lynne/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3
> predictions/Alginate/fold_alg844ijf/fold_alg844ijf_model_0.cif"
Chain information for fold_alg844ijf_model_0.cif #16
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
> open "/Users/lynne/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3
> predictions/Alginate/fold_alg844ijf/fold_alg844ijf_model_1.cif"
Chain information for fold_alg844ijf_model_1.cif #17
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
> open "/Users/lynne/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3
> predictions/Alginate/fold_alg844ijf/fold_alg844ijf_model_2.cif"
Chain information for fold_alg844ijf_model_2.cif #18
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
> open "/Users/lynne/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3
> predictions/Alginate/fold_alg844ijf/fold_alg844ijf_model_3.cif"
Chain information for fold_alg844ijf_model_3.cif #19
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
> open "/Users/lynne/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3
> predictions/Alginate/fold_alg844ijf/fold_alg844ijf_model_4.cif"
Chain information for fold_alg844ijf_model_4.cif #20
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
> hide #11-20 atoms
> show #11-20 cartoons
Computing secondary structure
[Repeated 4 time(s)]
> ui tool show Matchmaker
> matchmaker #16-20 to #11
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_algkxijf_model_0.cif, chain C (#11) with
fold_alg844ijf_model_0.cif, chain D (#16), sequence alignment score = 2672.2
RMSD between 448 pruned atom pairs is 0.473 angstroms; (across all 520 pairs:
4.351)
Matchmaker fold_algkxijf_model_0.cif, chain C (#11) with
fold_alg844ijf_model_1.cif, chain D (#17), sequence alignment score = 2684.2
RMSD between 452 pruned atom pairs is 0.498 angstroms; (across all 520 pairs:
3.450)
Matchmaker fold_algkxijf_model_0.cif, chain C (#11) with
fold_alg844ijf_model_2.cif, chain D (#18), sequence alignment score = 2669.2
RMSD between 450 pruned atom pairs is 0.473 angstroms; (across all 520 pairs:
4.341)
Matchmaker fold_algkxijf_model_0.cif, chain C (#11) with
fold_alg844ijf_model_3.cif, chain D (#19), sequence alignment score = 2669.8
RMSD between 454 pruned atom pairs is 0.534 angstroms; (across all 520 pairs:
5.088)
Matchmaker fold_algkxijf_model_0.cif, chain C (#11) with
fold_alg844ijf_model_4.cif, chain D (#20), sequence alignment score = 2653.6
RMSD between 454 pruned atom pairs is 0.503 angstroms; (across all 520 pairs:
3.340)
> hide #12 models
> hide #13 models
> hide #14 models
> hide #15 models
> hide #16 models
> hide #17 models
> hide #18 models
> hide #19 models
> hide #20 models
> show #12 models
> show #13 models
> show #14 models
> show #15 models
> hide #15 models
> hide #14 models
> hide #13 models
> hide #12 models
> hide #11 models
> show #11 models
> show #16 models
> show #17 models
> show #18 models
> show #19 models
> delete #16
> delete #17
> delete #18
> delete #19
> delete #20
> open "/Users/lynne/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3 predictions/Alginate/7ula_XK structure.cif"
Summary of feedback from opening /Users/lynne/SickKids Research Dropbox/Howell
Lab's shared workspace/Alphafold 3 predictions/Alginate/7ula_XK structure.cif
---
note | Fetching CCD NI from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/I/NI/NI.cif
7ula_XK structure.cif title:
Structure of the Pseudomonas putida AlgKX modification and secretion complex
[more info...]
Chain information for 7ula_XK structure.cif #16
---
Chain | Description | UniProt
A | Alginate biosynthesis protein AlgX | ALGX_PSEPK 1-479
B | Alginate biosynthesis protein AlgK | ALGK_PSEPK 33-484
Non-standard residues in 7ula_XK structure.cif #16
---
CL — chloride ion
GOL — glycerol (glycerin; propane-1,2,3-triol)
NI — nickel (II) ion
16 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
5622 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> ui tool show Matchmaker
[Repeated 1 time(s)]
> matchmaker #!16 to #11
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_algkxijf_model_0.cif, chain B (#11) with 7ula_XK
structure.cif, chain A (#16), sequence alignment score = 1396.4
RMSD between 389 pruned atom pairs is 0.767 angstroms; (across all 420 pairs:
1.711)
> hide #11 models
> ui tool show "Show Sequence Viewer"
> sequence chain #16/A
Alignment identifier is 16/A
> select clear
> select #16/A:29
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #16/A:29-33
36 atoms, 37 bonds, 5 residues, 1 model selected
> show #10 models
> show #11 models
> hide #10 models
> show #6 models
> ui tool show Matchmaker
> matchmaker #6-15 to #16
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7ula_XK structure.cif, chain A (#16) with
fold_alg844kxijf_model_0.cif, chain D (#6), sequence alignment score = 1405.4
RMSD between 390 pruned atom pairs is 0.803 angstroms; (across all 420 pairs:
1.768)
Matchmaker 7ula_XK structure.cif, chain A (#16) with
fold_alg844kxijf_model_1.cif, chain D (#7), sequence alignment score = 1394
RMSD between 388 pruned atom pairs is 0.827 angstroms; (across all 420 pairs:
1.725)
Matchmaker 7ula_XK structure.cif, chain A (#16) with
fold_alg844kxijf_model_2.cif, chain D (#8), sequence alignment score = 1384.4
RMSD between 391 pruned atom pairs is 0.798 angstroms; (across all 420 pairs:
1.696)
Matchmaker 7ula_XK structure.cif, chain A (#16) with
fold_alg844kxijf_model_3.cif, chain D (#9), sequence alignment score = 1394
RMSD between 383 pruned atom pairs is 0.863 angstroms; (across all 420 pairs:
1.773)
Matchmaker 7ula_XK structure.cif, chain A (#16) with
fold_alg844kxijf_model_4.cif, chain D (#10), sequence alignment score = 1387.4
RMSD between 388 pruned atom pairs is 0.818 angstroms; (across all 420 pairs:
1.732)
Matchmaker 7ula_XK structure.cif, chain A (#16) with
fold_algkxijf_model_0.cif, chain B (#11), sequence alignment score = 1396.4
RMSD between 389 pruned atom pairs is 0.767 angstroms; (across all 420 pairs:
1.711)
Matchmaker 7ula_XK structure.cif, chain A (#16) with
fold_algkxijf_model_1.cif, chain B (#12), sequence alignment score = 1405.4
RMSD between 387 pruned atom pairs is 0.819 angstroms; (across all 420 pairs:
1.760)
Matchmaker 7ula_XK structure.cif, chain A (#16) with
fold_algkxijf_model_2.cif, chain B (#13), sequence alignment score = 1396.4
RMSD between 388 pruned atom pairs is 0.822 angstroms; (across all 420 pairs:
1.753)
Matchmaker 7ula_XK structure.cif, chain A (#16) with
fold_algkxijf_model_3.cif, chain B (#14), sequence alignment score = 1419.8
RMSD between 390 pruned atom pairs is 0.832 angstroms; (across all 420 pairs:
1.776)
Matchmaker 7ula_XK structure.cif, chain A (#16) with
fold_algkxijf_model_4.cif, chain B (#15), sequence alignment score = 1399.4
RMSD between 392 pruned atom pairs is 0.791 angstroms; (across all 420 pairs:
1.771)
> hide #11 models
> hide #6 models
> show #11 models
> show #12 models
> show #13 models
> show #14 models
> show #15 models
> hide #11 models
> show #11 models
> hide #12 models
> hide #13 models
> hide #14 models
> hide #15 models
> show #6 models
> delete #6
> delete #7
> delete #8
> delete #9
> delete #10
> open "/Users/lynne/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3
> predictions/Alginate/fold_algekx_minus_ss/fold_algekx_minus_ss_model_4.cif"
Chain information for fold_algekx_minus_ss_model_4.cif #6
---
Chain | Description
A | .
B | .
C | .
> open "/Users/lynne/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3
> predictions/Alginate/fold_algekx_minus_ss/fold_algekx_minus_ss_model_1.cif"
Chain information for fold_algekx_minus_ss_model_1.cif #7
---
Chain | Description
A | .
B | .
C | .
> open "/Users/lynne/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3
> predictions/Alginate/fold_algekx_minus_ss/fold_algekx_minus_ss_model_0.cif"
Chain information for fold_algekx_minus_ss_model_0.cif #8
---
Chain | Description
A | .
B | .
C | .
> open "/Users/lynne/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3
> predictions/Alginate/fold_algekx_minus_ss/fold_algekx_minus_ss_model_2.cif"
Chain information for fold_algekx_minus_ss_model_2.cif #9
---
Chain | Description
A | .
B | .
C | .
> open "/Users/lynne/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3
> predictions/Alginate/fold_algekx_minus_ss/fold_algekx_minus_ss_model_3.cif"
Chain information for fold_algekx_minus_ss_model_3.cif #10
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
[Repeated 4 time(s)]
> ui tool show Matchmaker
> matchmaker #6-10 to #16
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7ula_XK structure.cif, chain A (#16) with
fold_algekx_minus_ss_model_4.cif, chain C (#6), sequence alignment score =
1390.2
RMSD between 390 pruned atom pairs is 0.758 angstroms; (across all 420 pairs:
1.653)
Matchmaker 7ula_XK structure.cif, chain A (#16) with
fold_algekx_minus_ss_model_1.cif, chain C (#7), sequence alignment score =
1403.4
RMSD between 387 pruned atom pairs is 0.749 angstroms; (across all 420 pairs:
1.576)
Matchmaker 7ula_XK structure.cif, chain A (#16) with
fold_algekx_minus_ss_model_0.cif, chain C (#8), sequence alignment score =
1384.2
RMSD between 385 pruned atom pairs is 0.763 angstroms; (across all 420 pairs:
1.688)
Matchmaker 7ula_XK structure.cif, chain A (#16) with
fold_algekx_minus_ss_model_2.cif, chain C (#9), sequence alignment score =
1383
RMSD between 386 pruned atom pairs is 0.755 angstroms; (across all 420 pairs:
1.632)
Matchmaker 7ula_XK structure.cif, chain A (#16) with
fold_algekx_minus_ss_model_3.cif, chain C (#10), sequence alignment score =
1377.6
RMSD between 391 pruned atom pairs is 0.744 angstroms; (across all 420 pairs:
1.608)
> hide #11 models
> color sel bypolymer
> color sel bychain
> color sel bypolymer
[Repeated 2 time(s)]
> hide #7 models
> hide #8 models
> hide #9 models
> hide #10 models
> open "/Users/lynne/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3 predictions/Alginate/AlgE_3RBH.pdb"
AlgE_3RBH.pdb title:
Structure of alginate export protein ALGE from pseudomonas aeruginosa [more
info...]
Chain information for AlgE_3RBH.pdb #17
---
Chain | Description | UniProt
A B C D | alginate production protein ALGE | ALGE_PSEAE 33-490
Non-standard residues in AlgE_3RBH.pdb #17
---
C8E — (hydroxyethyloxy)tri(ethyloxy)octane
CA — calcium ion
EDO — 1,2-ethanediol (ethylene glycol)
65 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
12898 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> ui tool show Matchmaker
> matchmaker #!17 to #6
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_algekx_minus_ss_model_4.cif, chain A (#6) with AlgE_3RBH.pdb,
chain B (#17), sequence alignment score = 2343.2
RMSD between 407 pruned atom pairs is 0.512 angstroms; (across all 429 pairs:
3.730)
> save "/Users/lynne/SickKids Research Dropbox/Howell Lab's shared
> workspace/Grants/CIHR 2026 PNAG-alginate/Alginate Section/Alginate
> models.cxs"
——— End of log from Thu Dec 18 15:12:06 2025 ———
> view name session-start
opened ChimeraX session
> hide #!17 models
> hide #!16 models
> hide #6 models
> show #1 models
> color #1 bychain
> open "/Users/lynne/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3
> predictions/Alginate/fold_alg844_dimer_g/fold_alg844_dimer_g_model_0.cif"
Chain information for fold_alg844_dimer_g_model_0.cif #18
---
Chain | Description
A | .
B C | .
D | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #18 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_alg844_model_0.cif, chain A (#1) with
fold_alg844_dimer_g_model_0.cif, chain A (#18), sequence alignment score =
2611.5
RMSD between 487 pruned atom pairs is 0.632 angstroms; (across all 494 pairs:
0.691)
> color #1,18 bychain
> hide #1 models
> open "/Users/lynne/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3
> predictions/Alginate/fold_alg8_44/fold_alg8_44_model_0.cif"
Chain information for fold_alg8_44_model_0.cif #19
---
Chain | Description
A | .
B C | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #19 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_alg844_model_0.cif, chain A (#1) with
fold_alg8_44_model_0.cif, chain A (#19), sequence alignment score = 2610.9
RMSD between 494 pruned atom pairs is 0.597 angstroms; (across all 494 pairs:
0.597)
> color #18-19 bychain
> hide #18 models
> show #18 models
> color #18 #00fdffff
> hide #18 models
> show #18 models
> hide #18 models
> show #1 models
> show #18 models
> show #6 models
> hide #18 models
> hide #19 models
> hide #1 models
> color #6 bychain
> coulombic #6
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for fold_algekx_minus_ss_model_4.cif_A SES surface #6.1:
minimum, -22.15, mean -5.51, maximum 11.22
Coulombic values for fold_algekx_minus_ss_model_4.cif_B SES surface #6.2:
minimum, -19.50, mean -2.49, maximum 10.83
Coulombic values for fold_algekx_minus_ss_model_4.cif_C SES surface #6.3:
minimum, -26.63, mean -1.36, maximum 11.86
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!6 surfaces
> show #!17 models
> hide #!6 models
> show #!17 surfaces
> hide #!17 surfaces
> hide #!17 models
> show #!16 models
> color sel bychain
> save "/Users/lynne/SickKids Research Dropbox/Howell Lab's shared
> workspace/Grants/CIHR 2026 PNAG-alginate/Alginate Section/Alginate
> models.cxs"
——— End of log from Fri Dec 19 16:32:43 2025 ———
> view name session-start
opened ChimeraX session
> open "/Users/lynnehowell/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3
> predictions/Alginate/fold_algg_x/fold_algg_x_model_0.cif"
Chain information for fold_algg_x_model_0.cif #20
---
Chain | Description
A | .
B | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #20 to #16
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7ula_XK structure.cif, chain A (#16) with fold_algg_x_model_0.cif,
chain B (#20), sequence alignment score = 1387.8
RMSD between 383 pruned atom pairs is 0.757 angstroms; (across all 420 pairs:
3.300)
> open "/Users/lynnehowell/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3
> predictions/Alginate/fold_algekx_minus_ss/fold_algekx_minus_ss_model_0.cif"
Chain information for fold_algekx_minus_ss_model_0.cif #21
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #21 to #16
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7ula_XK structure.cif, chain A (#16) with
fold_algekx_minus_ss_model_0.cif, chain C (#21), sequence alignment score =
1384.2
RMSD between 385 pruned atom pairs is 0.763 angstroms; (across all 420 pairs:
1.688)
> color sel bypolymer
[Repeated 1 time(s)]
> hide #20 models
> hide #!16 models
> select add #16
5686 atoms, 5767 bonds, 7 pseudobonds, 784 residues, 4 models selected
> select subtract #16
Nothing selected
> show #!16 models
> color #21#!16 bychain
> ui mousemode right translate
> select #16/A:104
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
50 atoms, 50 bonds, 6 residues, 1 model selected
> select up
1716 atoms, 1761 bonds, 220 residues, 1 model selected
> ui tool show "Color Actions"
> color sel turquoise
> color sel dark turquoise
> color sel teal
> color sel dark cyan
> select clear
> hide #21 models
> show #21 models
> hide #!16 models
> show #!16 models
> select #16/A:242
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
74 atoms, 75 bonds, 9 residues, 1 model selected
> select up
1716 atoms, 1761 bonds, 220 residues, 1 model selected
> color sel light sea green
> align #6/A:59-161@CA toAtoms #14/A:59-161@CA
RMSD between 103 atom pairs is 16.130 angstroms
> select #16/A:284
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
90 atoms, 92 bonds, 11 residues, 1 model selected
> select up
1607 atoms, 1640 bonds, 210 residues, 1 model selected
> color sel light sea green
> hide #!16 models
> select #21/C:197
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
75 atoms, 76 bonds, 10 residues, 1 model selected
> select up
3526 atoms, 3613 bonds, 448 residues, 1 model selected
> color sel light sea green
> select clear
> show #!16 models
> show #20 models
> select clear
[Repeated 1 time(s)]
> hide #21 models
> hide #!16 models
> select #20/B:197
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
75 atoms, 76 bonds, 10 residues, 1 model selected
> select up
3526 atoms, 3613 bonds, 448 residues, 1 model selected
> color sel light sea green
> select clear
> show #21 models
> show #!16 models
> open "/Users/lynnehowell/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3
> predictions/Alginate/fold_algg_x_44/fold_algg_x_44_model_0.cif"
Chain information for fold_algg_x_44_model_0.cif #22
---
Chain | Description
A | .
B | .
C | .
> open "/Users/lynnehowell/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3
> predictions/Alginate/fold_algg_x_44/fold_algg_x_44_model_1.cif"
Chain information for fold_algg_x_44_model_1.cif #23
---
Chain | Description
A | .
B | .
C | .
> open "/Users/lynnehowell/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3
> predictions/Alginate/fold_algg_x_44/fold_algg_x_44_model_2.cif"
Chain information for fold_algg_x_44_model_2.cif #24
---
Chain | Description
A | .
B | .
C | .
> open "/Users/lynnehowell/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3
> predictions/Alginate/fold_algg_x_44/fold_algg_x_44_model_3.cif"
Chain information for fold_algg_x_44_model_3.cif #25
---
Chain | Description
A | .
B | .
C | .
> open "/Users/lynnehowell/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3
> predictions/Alginate/fold_algg_x_44/fold_algg_x_44_model_4.cif"
Chain information for fold_algg_x_44_model_4.cif #26
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
[Repeated 4 time(s)]
> ui tool show Matchmaker
> matchmaker #22-26 to #20
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_algg_x_model_0.cif, chain A (#20) with
fold_algg_x_44_model_0.cif, chain A (#22), sequence alignment score = 2572
RMSD between 467 pruned atom pairs is 0.290 angstroms; (across all 508 pairs:
3.356)
Matchmaker fold_algg_x_model_0.cif, chain A (#20) with
fold_algg_x_44_model_1.cif, chain A (#23), sequence alignment score = 2546.8
RMSD between 447 pruned atom pairs is 0.263 angstroms; (across all 508 pairs:
10.270)
Matchmaker fold_algg_x_model_0.cif, chain A (#20) with
fold_algg_x_44_model_2.cif, chain A (#24), sequence alignment score = 2564.8
RMSD between 453 pruned atom pairs is 0.225 angstroms; (across all 508 pairs:
3.933)
Matchmaker fold_algg_x_model_0.cif, chain A (#20) with
fold_algg_x_44_model_3.cif, chain A (#25), sequence alignment score = 2582.8
RMSD between 446 pruned atom pairs is 0.355 angstroms; (across all 508 pairs:
8.046)
Matchmaker fold_algg_x_model_0.cif, chain A (#20) with
fold_algg_x_44_model_4.cif, chain A (#26), sequence alignment score = 2575.6
RMSD between 454 pruned atom pairs is 0.234 angstroms; (across all 508 pairs:
11.699)
> hide #26 models
> hide #24 models
> show #24 models
> hide #24 models
> show #24 models
> hide #24 models
> hide #23 models
> show #23 models
> hide #21 models
> hide #!16 models
> hide #20 models
> show #20 models
> open "/Users/lynnehowell/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3
> predictions/Alginate/fold_algg_44/fold_algg_44_model_0.cif"
Chain information for fold_algg_44_model_0.cif #27
---
Chain | Description
A | .
B | .
> open "/Users/lynnehowell/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3
> predictions/Alginate/fold_algg_44/fold_algg_44_model_1.cif"
Chain information for fold_algg_44_model_1.cif #28
---
Chain | Description
A | .
B | .
> open "/Users/lynnehowell/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3
> predictions/Alginate/fold_algg_44/fold_algg_44_model_2.cif"
Chain information for fold_algg_44_model_2.cif #29
---
Chain | Description
A | .
B | .
> open "/Users/lynnehowell/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3
> predictions/Alginate/fold_algg_44/fold_algg_44_model_3.cif"
Chain information for fold_algg_44_model_3.cif #30
---
Chain | Description
A | .
B | .
> open "/Users/lynnehowell/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3
> predictions/Alginate/fold_algg_44/fold_algg_44_model_4.cif"
Chain information for fold_algg_44_model_4.cif #31
---
Chain | Description
A | .
B | .
Computing secondary structure
[Repeated 4 time(s)]
> save "/Users/lynnehowell/SickKids Research Dropbox/Howell Lab's shared
> workspace/Grants/CIHR 2026 PNAG-alginate/Alginate Section/Alginate
> models.cxs"
> ui tool show Matchmaker
> matchmaker #27-31 to #22
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_algg_x_44_model_0.cif, chain A (#22) with
fold_algg_44_model_0.cif, chain A (#27), sequence alignment score = 2564.8
RMSD between 456 pruned atom pairs is 0.232 angstroms; (across all 508 pairs:
4.454)
Matchmaker fold_algg_x_44_model_0.cif, chain A (#22) with
fold_algg_44_model_1.cif, chain A (#28), sequence alignment score = 2557.6
RMSD between 475 pruned atom pairs is 0.241 angstroms; (across all 508 pairs:
1.783)
Matchmaker fold_algg_x_44_model_0.cif, chain A (#22) with
fold_algg_44_model_2.cif, chain A (#29), sequence alignment score = 2564.8
RMSD between 452 pruned atom pairs is 0.240 angstroms; (across all 508 pairs:
6.558)
Matchmaker fold_algg_x_44_model_0.cif, chain A (#22) with
fold_algg_44_model_3.cif, chain A (#30), sequence alignment score = 2552.8
RMSD between 456 pruned atom pairs is 0.244 angstroms; (across all 508 pairs:
8.914)
Matchmaker fold_algg_x_44_model_0.cif, chain A (#22) with
fold_algg_44_model_4.cif, chain A (#31), sequence alignment score = 2560
RMSD between 456 pruned atom pairs is 0.187 angstroms; (across all 508 pairs:
3.763)
> show #19 models
> ui tool show Matchmaker
> matchmaker #19 to #22
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_algg_x_44_model_0.cif, chain C (#22) with
fold_alg8_44_model_0.cif, chain C (#19), sequence alignment score = 1934.8
RMSD between 86 pruned atom pairs is 0.309 angstroms; (across all 389 pairs:
71.368)
> hide #19 models
> hide #22 models
> hide #23 models
> hide #25 models
> show #25 models
> hide #25 models
> hide #20 models
> color #27-31 bypolymer
> hide #31 models
> hide #30 models
> hide #29 models
> hide #28 models
> show #22 models
> color #22,27 bychain
> show #23 models
> hide #23 models
> show #!16 models
> show #19 models
> hide #!16 models
> hide #22 models
> hide #27 models
> show #25 models
> hide #19 models
> color #25 bypolymer
> select #25/C:259
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
52 atoms, 51 bonds, 7 residues, 1 model selected
> color sel red
> hide sel surfaces
> show sel surfaces
> select clear
> select #25/A:252
14 atoms, 15 bonds, 1 residue, 1 model selected
> select up
42 atoms, 43 bonds, 5 residues, 1 model selected
> select up
3954 atoms, 4037 bonds, 508 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> select clear
> open "/Users/lynnehowell/SickKids Research Dropbox/Howell Lab's shared
> workspace/Alphafold 3 predictions/Alginate/4ozy.cif"
4ozy.cif title:
Crystal Structure of the periplasmic alginate epimerase AlgG T265N mutant
[more info...]
Chain information for 4ozy.cif #32
---
Chain | Description | UniProt
A | Poly(beta-D-mannuronate) C5 epimerase | ALGG_PSESM 69-491
4ozy.cif mmCIF Assemblies
---
1| author_defined_assembly
2| software_defined_assembly
3261 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> ui tool show Matchmaker
> matchmaker #32 to #20
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_algg_x_model_0.cif, chain A (#20) with 4ozy.cif, chain A
(#32), sequence alignment score = 1605.6
RMSD between 405 pruned atom pairs is 0.517 angstroms; (across all 423 pairs:
0.920)
> save "/Users/lynnehowell/SickKids Research Dropbox/Howell Lab's shared
> workspace/Grants/CIHR 2026 PNAG-alginate/Alginate Section/Alginate
> models.cxs"
——— End of log from Sat Dec 20 13:53:51 2025 ———
> view name session-start
opened ChimeraX session
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M3 Max
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,10
Model Number: MRX83LL/A
Chip: Apple M3 Max
Total Number of Cores: 14 (10 performance and 4 efficiency)
Memory: 36 GB
System Firmware Version: 13822.61.10
OS Loader Version: 13822.61.10
Software:
System Software Overview:
System Version: macOS 26.2 (25C56)
Kernel Version: Darwin 25.2.0
Time since boot: 2 days, 4 hours, 17 minutes
Graphics/Displays:
Apple M3 Max:
Chipset Model: Apple M3 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 30
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
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
appnope: 0.1.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2025.7.14
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-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-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-ListInfo: 1.2.2
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-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
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
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
joblib: 1.5.0
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
llvmlite: 0.44.0
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
msgpack: 1.1.1
multidict: 6.7.0
narwhals: 1.43.1
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numba: 0.61.2
numexpr: 2.14.1
numpy: 2.2.6
numpy: 1.26.4
OpenMM: 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
plotly: 6.0.1
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
pyKVFinder: 0.8.1
pynmrstar: 3.3.6
pynndescent: 0.5.13
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-commercial: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 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
scikit-learn: 1.6.1
scipy: 1.14.0
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
tables: 3.10.2
tcia_utils: 1.5.1
threadpoolctl: 3.6.0
tifffile: 2025.3.13
tinyarray: 1.2.5
tomlkit: 0.13.2
tornado: 6.5.4
tqdm: 4.67.1
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
tzdata: 2025.3
umap-learn: 0.5.7
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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