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Opened 18 months ago
Last modified 18 months ago
#15207 assigned defect
ISOLDE: ResidueStepper holding reference to closed structure
| Reported by: | Owned by: | Tristan Croll | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.0-arm64-arm-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/cryoem/cas1-2-3-prespacer-
> bound/isolde/chimeraXsessions/20240513-Combined-model-fullactiveCas1-rigid-
> body-docked-local-refinement-J1222-preisolde.cxs
Opened cryosparc_P29_J1222_004_volume_map_flipped.mrc as #2, grid size
270,270,270, pixel 1.67, shown at level 0.712, step 1, values float32
Log from Tue May 14 15:03:45 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/cryoem/cas1-2-3-prespacer-
> bound/isolde/chimeraXsessions/20240513-Combined-model-fullactiveCas1-rigid-
> body-docked-local-refinement-J1446-preisolde.cxs
Opened cryosparc_P29_J1146_004_volume_map.mrc as #1, grid size 270,270,270,
pixel 1.67, shown at level 0.874, step 1, values float32
Log from Mon May 13 09:07:39 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/cryoem/cas1-2-3-prespacer-
> bound/isolde/chimeraXsessions/20240510-Combined-model-fullCas1-rigid-body-
> docked-local-refinement-J1446-preisolde.cxs
Opened cryosparc_P29_J1146_004_volume_map.mrc as #1, grid size 270,270,270,
pixel 1.67, shown at level 1.05, step 1, values float32
Log from Fri May 10 14:39:35 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/cryoem/cas1-2-3-prespacer-
> bound/isolde/chimeraXsessions/20240510-Combined-model-fullCas1-rigid-body-
> docked-local-refinement-J1446-preisolde.cxs format session
Opened cryosparc_P29_J1146_004_volume_map.mrc as #1, grid size 270,270,270,
pixel 1.67, shown at level 1.05, step 1, values float32
Log from Fri May 10 14:36:54 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/cryoem/cas1-2-3-prespacer-bound/isolde/chimeraXsessions/Alphafold-
> fragments-rigid-body-docked-local-refinement-J1446.cxs
Opened cryosparc_P29_J1146_004_volume_map.mrc as #1, grid size 270,270,270,
pixel 1.67, shown at level 1.05, step 1, values float32
Log from Thu Apr 18 10:27:35 2024 Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/cryoem/cas1-2-3-prespacer-
> bound/cryosparc/P6-P29/J1146/cryosparc_P29_J1146_004_volume_map.mrc format
> mrc
Opened cryosparc_P29_J1146_004_volume_map.mrc as #1, grid size 270,270,270,
pixel 1.67, shown at level 0.19, step 2, values float32
> volume #1 level 0.3726
> set bgColor white
> lighting simple
> lighting soft
> transparency 50
> graphics silhouettes true
> volume #1 level 0.5901
> volume #1 step 1
> transparency 0
> open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/AlphaFold/Cas1-AF-Q02ML7-F1-model_v4.pdb
Cas1-AF-Q02ML7-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for crispr-associated endonuclease CAS1
(Q02ML7) [more info...]
Chain information for Cas1-AF-Q02ML7-F1-model_v4.pdb #2
---
Chain | Description | UniProt
A | crispr-associated endonuclease CAS1 | CAS1_PSEAB 1-324
> select add #2
2549 atoms, 2602 bonds, 324 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,-47.956,0,1,0,244.74,0,0,1,175.27
> view matrix models #2,1,0,0,142.44,0,1,0,321.71,0,0,1,135.56
> view matrix models #2,1,0,0,239.01,0,1,0,241.92,0,0,1,201.51
> view matrix models #2,1,0,0,228.14,0,1,0,235.99,0,0,1,195.79
> view matrix models #2,1,0,0,281.59,0,1,0,280.2,0,0,1,262.22
> undo
> view matrix models #2,1,0,0,305.29,0,1,0,239.74,0,0,1,248.42
> view matrix models
> #2,0.67637,-0.35627,-0.64466,303.86,0.63924,-0.15086,0.75406,256.9,-0.3659,-0.92212,0.1257,251.04
> view matrix models
> #2,0.67637,-0.35627,-0.64466,228.74,0.63924,-0.15086,0.75406,260.81,-0.3659,-0.92212,0.1257,229.99
> view matrix models
> #2,0.69767,0.425,-0.57674,222.42,0.56347,-0.82269,0.075372,264.52,-0.44245,-0.37756,-0.81344,222.85
> view matrix models
> #2,0.69767,0.425,-0.57674,226.8,0.56347,-0.82269,0.075372,278.73,-0.44245,-0.37756,-0.81344,215.17
> fitmap #2 inMap #1
Fit molecule Cas1-AF-Q02ML7-F1-model_v4.pdb (#2) to map
cryosparc_P29_J1146_004_volume_map.mrc (#1) using 2549 atoms
average map value = 0.6987, steps = 104
shifted from previous position = 1.12
rotated from previous position = 40.6 degrees
atoms outside contour = 1043, contour level = 0.59008
Position of Cas1-AF-Q02ML7-F1-model_v4.pdb (#2) relative to
cryosparc_P29_J1146_004_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.39886013 0.00699683 -0.91698508 226.89256781
0.70554277 -0.64109819 0.30199753 279.93068950
-0.58576445 -0.76742697 -0.26064507 217.53697864
Axis -0.81041609 -0.25100092 0.52936217
Axis point 0.00000000 172.48948470 125.91726469
Rotation angle (degrees) 138.71540528
Shift along axis -138.98440016
> delete #1:1-116
> select add #1
2549 atoms, 2602 bonds, 324 residues, 3 models selected
> select subtract #1
2549 atoms, 2602 bonds, 324 residues, 1 model selected
> hide #!1 models
> delete #2:1-116
> open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/AlphaFold/Cas1-AF-Q02ML7-F1-model_v4.pdb
Cas1-AF-Q02ML7-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for crispr-associated endonuclease CAS1
(Q02ML7) [more info...]
Chain information for Cas1-AF-Q02ML7-F1-model_v4.pdb #3
---
Chain | Description | UniProt
A | crispr-associated endonuclease CAS1 | CAS1_PSEAB 1-324
> delete #3:1-116
> show #!1 models
> select add #3
3296 atoms, 3360 bonds, 416 residues, 2 models selected
> view matrix models
> #2,0.39886,0.0069968,-0.91699,293.11,0.70554,-0.6411,0.302,436.44,-0.58576,-0.76743,-0.26065,253.37,#3,1,0,0,66.222,0,1,0,156.5,0,0,1,35.836
> undo
> select subtract #2
1648 atoms, 1680 bonds, 208 residues, 1 model selected
> view matrix models #3,1,0,0,110.2,0,1,0,319.82,0,0,1,104.79
> view matrix models #3,1,0,0,186.81,0,1,0,216.62,0,0,1,196.51
> view matrix models #3,1,0,0,225.41,0,1,0,298.37,0,0,1,260.17
> view matrix models #3,1,0,0,222.49,0,1,0,299.48,0,0,1,259.94
> view matrix models
> #3,1,0.001374,0.0022492,222.59,-0.0013732,1,-0.00035237,299.54,-0.0022497,0.00034928,1,259.94
> view matrix models
> #3,0.45961,0.52749,-0.7145,222.43,0.77349,0.15759,0.6139,298.81,0.43643,-0.83481,-0.33558,255.62
> view matrix models
> #3,0.45961,0.52749,-0.7145,267.52,0.77349,0.15759,0.6139,271.04,0.43643,-0.83481,-0.33558,211
> view matrix models
> #3,-0.43231,-0.85821,-0.27673,266.24,-0.52494,-0.010005,0.85108,271.49,-0.73318,0.5132,-0.44618,213.69
> view matrix models
> #3,-0.43231,-0.85821,-0.27673,260.76,-0.52494,-0.010005,0.85108,248.71,-0.73318,0.5132,-0.44618,225.63
> fitmap #3 inMap #1
Fit molecule Cas1-AF-Q02ML7-F1-model_v4.pdb (#3) to map
cryosparc_P29_J1146_004_volume_map.mrc (#1) using 1648 atoms
average map value = 0.4753, steps = 104
shifted from previous position = 11.8
rotated from previous position = 37.7 degrees
atoms outside contour = 1041, contour level = 0.59008
Position of Cas1-AF-Q02ML7-F1-model_v4.pdb (#3) relative to
cryosparc_P29_J1146_004_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.09531133 -0.99281764 -0.07231100 250.51622379
-0.76156796 -0.11950444 0.63697168 250.95743457
-0.64103820 -0.00564087 -0.76748823 218.22039258
Axis -0.72305147 0.63991753 0.26019631
Axis point 0.00000000 270.17760014 117.26689640
Rotation angle (degrees) 153.61661691
Shift along axis 36.23608003
> volume #1 level 0.4764
> view matrix models
> #3,0.40575,-0.88579,0.22525,276.28,0.8603,0.28692,-0.42137,264.99,0.30862,0.36476,0.87847,236.99
> view matrix models
> #3,0.40575,-0.88579,0.22525,247.14,0.8603,0.28692,-0.42137,240.09,0.30862,0.36476,0.87847,222.28
> view matrix models
> #3,0.70571,-0.68015,0.19843,247.35,0.62255,0.46157,-0.63197,240.12,0.33824,0.56952,0.74916,222.41
> view matrix models
> #3,0.70571,-0.68015,0.19843,252.34,0.62255,0.46157,-0.63197,244.37,0.33824,0.56952,0.74916,224.93
> fitmap #3 inMap #1
Fit molecule Cas1-AF-Q02ML7-F1-model_v4.pdb (#3) to map
cryosparc_P29_J1146_004_volume_map.mrc (#1) using 1648 atoms
average map value = 0.7557, steps = 100
shifted from previous position = 4.96
rotated from previous position = 15 degrees
atoms outside contour = 451, contour level = 0.47644
Position of Cas1-AF-Q02ML7-F1-model_v4.pdb (#3) relative to
cryosparc_P29_J1146_004_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.78662923 -0.61679457 0.02790875 253.56939905
0.40922452 0.48699105 -0.77160547 242.04005943
0.46233075 0.61838836 0.63548886 220.57432268
Axis 0.78026517 -0.24386033 0.57595001
Axis point 0.00000000 90.06384661 337.82932909
Rotation angle (degrees) 62.96372151
Shift along axis 265.86718274
> open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/AlphaFold/Cas1-AF-Q02ML7-F1-model_v4.pdb
Cas1-AF-Q02ML7-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for crispr-associated endonuclease CAS1
(Q02ML7) [more info...]
Chain information for Cas1-AF-Q02ML7-F1-model_v4.pdb #4
---
Chain | Description | UniProt
A | crispr-associated endonuclease CAS1 | CAS1_PSEAB 1-324
> select add #4
4197 atoms, 4282 bonds, 532 residues, 2 models selected
> view matrix models
> #3,0.78663,-0.61679,0.027909,310.35,0.40922,0.48699,-0.77161,252.41,0.46233,0.61839,0.63549,230.93,#4,1,0,0,56.78,0,1,0,10.372,0,0,1,10.356
> undo
> select subtract #3
2549 atoms, 2602 bonds, 324 residues, 1 model selected
> view matrix models
> #4,0.27905,0.77037,0.57329,289.78,-0.92643,0.37309,-0.050407,142.37,-0.25272,-0.51704,0.8178,-38.161
> view matrix models
> #4,0.27905,0.77037,0.57329,311.9,-0.92643,0.37309,-0.050407,226.25,-0.25272,-0.51704,0.8178,103.1
> view matrix models
> #4,0.27905,0.77037,0.57329,224.92,-0.92643,0.37309,-0.050407,246.13,-0.25272,-0.51704,0.8178,92.949
> view matrix models
> #4,0.27905,0.77037,0.57329,234.07,-0.92643,0.37309,-0.050407,346.17,-0.25272,-0.51704,0.8178,196.84
> view matrix models
> #4,-0.25956,0.71888,0.64486,229.64,-0.80021,0.21373,-0.56035,347.72,-0.54065,-0.66147,0.51977,194.82
> view matrix models
> #4,-0.25956,0.71888,0.64486,211.49,-0.80021,0.21373,-0.56035,309.98,-0.54065,-0.66147,0.51977,170.03
> view matrix models
> #4,0.80425,0.24275,-0.54245,223.14,0.59186,-0.24471,0.768,329.36,0.053691,-0.93872,-0.34048,176.26
> view matrix models
> #4,0.8865,0.28156,-0.36721,223.81,0.4477,-0.32125,0.83448,328.72,0.11699,-0.90417,-0.41085,176.37
> view matrix models
> #4,0.8865,0.28156,-0.36721,209.76,0.4477,-0.32125,0.83448,325.14,0.11699,-0.90417,-0.41085,194.12
> delete #4:117-324
> view matrix models
> #4,0.8865,0.28156,-0.36721,206.65,0.4477,-0.32125,0.83448,298.12,0.11699,-0.90417,-0.41085,217.16
> view matrix models
> #4,0.8865,0.28156,-0.36721,200.66,0.4477,-0.32125,0.83448,282.71,0.11699,-0.90417,-0.41085,224.03
> fitmap #4 inMap #1
Fit molecule Cas1-AF-Q02ML7-F1-model_v4.pdb (#4) to map
cryosparc_P29_J1146_004_volume_map.mrc (#1) using 901 atoms
average map value = 0.5364, steps = 188
shifted from previous position = 29.9
rotated from previous position = 55.6 degrees
atoms outside contour = 476, contour level = 0.47644
Position of Cas1-AF-Q02ML7-F1-model_v4.pdb (#4) relative to
cryosparc_P29_J1146_004_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.25868995 0.94771751 -0.18684491 198.83742927
0.69074237 -0.04627682 0.72161860 260.24321163
0.67524400 -0.31573718 -0.66659999 233.79586403
Axis -0.75549715 -0.62785182 -0.18715274
Axis point 0.00000000 91.41151587 82.83386527
Rotation angle (degrees) 136.64327651
Shift along axis -357.37082221
> view matrix models
> #4,0.25869,0.94772,-0.18684,205.43,0.69074,-0.046277,0.72162,268.25,0.67524,-0.31574,-0.6666,222.46
> view matrix models
> #4,0.25869,0.94772,-0.18684,227.52,0.69074,-0.046277,0.72162,295.21,0.67524,-0.31574,-0.6666,190.83
> view matrix models
> #4,0.25573,0.81669,-0.51731,227.46,0.37467,0.40956,0.8318,283.71,0.89119,-0.40654,-0.20125,198.61
> view matrix models
> #4,0.25573,0.81669,-0.51731,214.32,0.37467,0.40956,0.8318,261.84,0.89119,-0.40654,-0.20125,230.5
> view matrix models
> #4,0.85586,0.47805,-0.1974,231,0.51175,-0.83803,0.18928,280.09,-0.074943,-0.26301,-0.96188,208.61
> fitmap #4 inMap #1
Fit molecule Cas1-AF-Q02ML7-F1-model_v4.pdb (#4) to map
cryosparc_P29_J1146_004_volume_map.mrc (#1) using 901 atoms
average map value = 0.5337, steps = 84
shifted from previous position = 6.46
rotated from previous position = 10.3 degrees
atoms outside contour = 437, contour level = 0.47644
Position of Cas1-AF-Q02ML7-F1-model_v4.pdb (#4) relative to
cryosparc_P29_J1146_004_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.91554757 0.31653229 -0.24815303 235.54852558
0.37128727 -0.90236201 0.21883450 272.79632577
-0.15465568 -0.29248946 -0.94367977 206.61577451
Axis -0.97827761 -0.17888143 0.10475858
Axis point 0.00000000 130.73970565 100.51041118
Rotation angle (degrees) 164.85047807
Shift along axis -257.58526967
> open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/AlphaFold/Cas1-AF-Q02ML7-F1-model_v4.pdb
Cas1-AF-Q02ML7-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for crispr-associated endonuclease CAS1
(Q02ML7) [more info...]
Chain information for Cas1-AF-Q02ML7-F1-model_v4.pdb #5
---
Chain | Description | UniProt
A | crispr-associated endonuclease CAS1 | CAS1_PSEAB 1-324
> view matrix models
> #4,0.79943,0.5517,-0.23777,230.02,0.58656,-0.80233,0.11047,273.71,-0.12983,-0.22778,-0.96502,205.8
> select add #5
3450 atoms, 3523 bonds, 440 residues, 2 models selected
> view matrix models
> #4,-0.33985,0.92188,0.18613,-41.735,0.90028,0.37613,-0.21914,273.37,-0.27203,0.093099,-0.95777,155.75,#5,0.19266,-0.91843,-0.34549,236.43,0.97933,0.20208,0.0089174,-9.0477,0.061627,-0.34007,0.93838,41.538
> undo
> select subtract #4
2549 atoms, 2602 bonds, 324 residues, 1 model selected
> view matrix models
> #5,0.95311,0.29753,0.055206,-2.8615,-0.29399,0.95366,-0.064004,-2.459,-0.071691,0.044773,0.99642,-1.0537
> view matrix models
> #5,0.95311,0.29753,0.055206,236.55,-0.29399,0.95366,-0.064004,150.54,-0.071691,0.044773,0.99642,75.794
> view matrix models
> #5,0.95311,0.29753,0.055206,238.73,-0.29399,0.95366,-0.064004,138.01,-0.071691,0.044773,0.99642,71.822
> view matrix models
> #5,0.92269,0.30913,-0.23042,237.8,-0.19399,0.88869,0.41544,140.41,0.33319,-0.33862,0.87995,78.621
> view matrix models
> #5,0.92269,0.30913,-0.23042,242.09,-0.19399,0.88869,0.41544,133.97,0.33319,-0.33862,0.87995,77.378
> view matrix models
> #5,0.92269,0.30913,-0.23042,221.4,-0.19399,0.88869,0.41544,161.52,0.33319,-0.33862,0.87995,94.78
> view matrix models
> #5,0.786,0.43026,-0.44393,218.69,-0.094296,0.79312,0.60173,163.62,0.61099,-0.4311,0.66396,97.733
> view matrix models
> #5,0.786,0.43026,-0.44393,226.24,-0.094296,0.79312,0.60173,156.59,0.61099,-0.4311,0.66396,93.308
Drag select of 1 cryosparc_P29_J1146_004_volume_map.mrc
> select subtract #1
Nothing selected
> select add #5
2549 atoms, 2602 bonds, 324 residues, 1 model selected
> view matrix models
> #5,0.26648,-0.41525,-0.8698,227.8,0.48731,0.83664,-0.25012,159.99,0.83158,-0.35721,0.4253,94.271
> view matrix models
> #5,0.26648,-0.41525,-0.8698,300.94,0.48731,0.83664,-0.25012,188.37,0.83158,-0.35721,0.4253,195.93
> view matrix models
> #5,0.0094385,-0.58698,-0.80955,300.13,0.59612,0.6533,-0.46673,190.53,0.80284,-0.47818,0.35607,196.56
> view matrix models
> #5,0.0094385,-0.58698,-0.80955,282.2,0.59612,0.6533,-0.46673,217.3,0.80284,-0.47818,0.35607,202.18
> view matrix models
> #5,0.22869,-0.96067,0.15752,289.27,0.91193,0.15478,-0.38004,224.64,0.34072,0.23056,0.91146,192.92
> view matrix models
> #5,0.22869,-0.96067,0.15752,278.95,0.91193,0.15478,-0.38004,245.21,0.34072,0.23056,0.91146,198.21
> view matrix models
> #5,0.22869,-0.96067,0.15752,255.88,0.91193,0.15478,-0.38004,244.25,0.34072,0.23056,0.91146,215.99
> fitmap #5 inMap #1
Fit molecule Cas1-AF-Q02ML7-F1-model_v4.pdb (#5) to map
cryosparc_P29_J1146_004_volume_map.mrc (#1) using 2549 atoms
average map value = 0.4235, steps = 100
shifted from previous position = 5.91
rotated from previous position = 27 degrees
atoms outside contour = 1515, contour level = 0.47644
Position of Cas1-AF-Q02ML7-F1-model_v4.pdb (#5) relative to
cryosparc_P29_J1146_004_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.00819339 -0.99580821 0.09109810 250.25510380
0.71407725 -0.05794810 -0.69766446 246.29565095
0.70001897 0.07076732 0.71060920 220.28776185
Axis 0.38986200 -0.30893452 0.86750624
Axis point -75.88283486 243.66198776 0.00000000
Rotation angle (degrees) 99.76297919
Shift along axis 212.57673475
> view matrix models
> #5,0.0081934,-0.99581,0.091098,279.34,0.71408,-0.057948,-0.69766,214.65,0.70002,0.070767,0.71061,219.63
> view matrix models
> #5,0.8196,-0.54231,0.18481,283.07,0.17032,-0.077358,-0.98235,212.47,0.54704,0.83661,0.028963,212.02
> view matrix models
> #5,0.56623,-0.65723,0.49743,282.3,0.5549,-0.1423,-0.81966,216.91,0.60949,0.74014,0.28412,213.91
> view matrix models
> #5,0.57526,-0.65467,0.49038,282.34,0.5455,-0.13968,-0.82639,216.78,0.60951,0.7429,0.27677,213.87
> view matrix models
> #5,0.57526,-0.65467,0.49038,257.28,0.5455,-0.13968,-0.82639,241.15,0.60951,0.7429,0.27677,212.91
> fitmap #5 inMap #1
Fit molecule Cas1-AF-Q02ML7-F1-model_v4.pdb (#5) to map
cryosparc_P29_J1146_004_volume_map.mrc (#1) using 2549 atoms
average map value = 0.7695, steps = 132
shifted from previous position = 9.32
rotated from previous position = 39.2 degrees
atoms outside contour = 752, contour level = 0.47644
Position of Cas1-AF-Q02ML7-F1-model_v4.pdb (#5) relative to
cryosparc_P29_J1146_004_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.80865163 -0.58753574 0.02973721 253.03519741
0.39847074 0.50984448 -0.76241699 242.16780506
0.43278588 0.62837915 0.64640237 220.79146719
Axis 0.79390236 -0.23007059 0.56283796
Axis point 0.00000000 84.05121419 344.90274225
Rotation angle (degrees) 61.15451188
Shift along axis 269.43936937
> select up
6746 atoms, 6883 bonds, 856 residues, 6 models selected
> select up
6746 atoms, 6883 bonds, 856 residues, 6 models selected
> delete #4:117-324
> transparency sel 50
> delete #5:117-324
> open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/AlphaFold/Cas23_AF-Q02ML8-F1-model_v4(1).pdb
Cas23_AF-Q02ML8-F1-model_v4(1).pdb title:
Alphafold monomer V2.0 prediction for crispr-associated nuclease/helicase CAS3
subtype I-F/ypest (Q02ML8) [more info...]
Chain information for Cas23_AF-Q02ML8-F1-model_v4(1).pdb #6
---
Chain | Description | UniProt
A | crispr-associated nuclease/helicase CAS3 subtype I-F/ypest | CAS3_PSEAB
1-1076
> select add #6
13635 atoms, 13938 bonds, 1724 residues, 7 models selected
> view matrix models
> #1,1,0,0,5.447,0,1,0,-1.5956,0,0,1,0.22628,#2,0.39886,0.0069968,-0.91699,232.34,0.70554,-0.6411,0.302,278.34,-0.58576,-0.76743,-0.26065,217.76,#3,0.78663,-0.61679,0.027909,259.02,0.40922,0.48699,-0.77161,240.44,0.46233,0.61839,0.63549,220.8,#4,0.79943,0.5517,-0.23777,235.47,0.58656,-0.80233,0.11047,272.11,-0.12983,-0.22778,-0.96502,206.02,#5,0.80865,-0.58754,0.029737,258.48,0.39847,0.50984,-0.76242,240.57,0.43279,0.62838,0.6464,221.02,#6,1,0,0,5.447,0,1,0,-1.5956,0,0,1,0.22628
> ~select
Nothing selected
> select add #6
8537 atoms, 8736 bonds, 1076 residues, 1 model selected
> view matrix models #6,1,0,0,78.924,0,1,0,-13.333,0,0,1,-19.737
> view matrix models #6,1,0,0,168.6,0,1,0,-60.157,0,0,1,17.331
> view matrix models
> #6,0.17182,-0.063587,-0.98307,151.87,-0.40842,0.90351,-0.12982,-63.811,0.89648,0.42381,0.12927,10.403
> view matrix models
> #6,0.17182,-0.063587,-0.98307,151.39,-0.40842,0.90351,-0.12982,-63.989,0.89648,0.42381,0.12927,10.59
> view matrix models
> #6,0.17182,-0.063587,-0.98307,277.8,-0.40842,0.90351,-0.12982,-36.716,0.89648,0.42381,0.12927,64.889
> view matrix models
> #6,0.17182,-0.063587,-0.98307,320.26,-0.40842,0.90351,-0.12982,13.789,0.89648,0.42381,0.12927,156.99
> view matrix models
> #6,0.17182,-0.063587,-0.98307,309.33,-0.40842,0.90351,-0.12982,115.06,0.89648,0.42381,0.12927,239.26
> view matrix models
> #6,0.17182,-0.063587,-0.98307,232.99,-0.40842,0.90351,-0.12982,179.09,0.89648,0.42381,0.12927,149.88
> view matrix models
> #6,0.17182,-0.063587,-0.98307,237.89,-0.40842,0.90351,-0.12982,208.15,0.89648,0.42381,0.12927,182.67
> view matrix models
> #6,0.67928,-0.68934,0.25179,259.8,-0.10206,-0.42849,-0.89776,202.93,0.72675,0.58413,-0.36142,174.4
> view matrix models
> #6,0.58357,-0.79603,0.16055,239.79,0.4676,0.16776,-0.86788,186.05,0.66393,0.58154,0.47012,177.93
> view matrix models
> #6,-0.065176,-0.81976,0.56899,238.36,0.96685,-0.19295,-0.16724,197.47,0.24688,0.53923,0.80516,177.75
> view matrix models
> #6,-0.065176,-0.81976,0.56899,237.97,0.96685,-0.19295,-0.16724,198.38,0.24688,0.53923,0.80516,177.81
> view matrix models
> #6,-0.065176,-0.81976,0.56899,228.95,0.96685,-0.19295,-0.16724,213,0.24688,0.53923,0.80516,183.06
> fitmap #6 inMap #1
Fit molecule Cas23_AF-Q02ML8-F1-model_v4(1).pdb (#6) to map
cryosparc_P29_J1146_004_volume_map.mrc (#1) using 8537 atoms
average map value = 0.7831, steps = 220
shifted from previous position = 5.03
rotated from previous position = 59 degrees
atoms outside contour = 2420, contour level = 0.47644
Position of Cas23_AF-Q02ML8-F1-model_v4(1).pdb (#6) relative to
cryosparc_P29_J1146_004_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.75327836 -0.27568339 0.59713515 229.17482003
0.65546641 0.23988014 -0.71611543 211.22699916
0.05418026 0.93083629 0.36139772 183.24573778
Axis 0.83672898 0.27584664 0.47306792
Axis point 0.00000000 50.71109588 111.43434095
Rotation angle (degrees) 79.78874249
Shift along axis 336.71114907
> delete #6:1-100
> open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/AlphaFold/Cas23_AF-Q02ML8-F1-model_v4(1).pdb
Cas23_AF-Q02ML8-F1-model_v4(1).pdb title:
Alphafold monomer V2.0 prediction for crispr-associated nuclease/helicase CAS3
subtype I-F/ypest (Q02ML8) [more info...]
Chain information for Cas23_AF-Q02ML8-F1-model_v4(1).pdb #7
---
Chain | Description | UniProt
A | crispr-associated nuclease/helicase CAS3 subtype I-F/ypest | CAS3_PSEAB
1-1076
> delete #7:101-1074
> delete #7:101-1076
> select subtract #6
Nothing selected
> select add #7
813 atoms, 824 bonds, 100 residues, 1 model selected
> view matrix models #7,1,0,0,-23.534,0,1,0,85.567,0,0,1,19.163
> view matrix models #7,1,0,0,96.397,0,1,0,175.21,0,0,1,56.983
> view matrix models #7,1,0,0,150.38,0,1,0,219.27,0,0,1,109.55
> view matrix models #7,1,0,0,256.92,0,1,0,70.781,0,0,1,206.85
> view matrix models
> #7,0.074549,0.15388,-0.98527,233.79,0.36173,0.91655,0.17052,78.246,0.9293,-0.36912,0.012664,215.56
> view matrix models
> #7,0.074549,0.15388,-0.98527,166.38,0.36173,0.91655,0.17052,112.59,0.9293,-0.36912,0.012664,225.03
> view matrix models
> #7,0.074549,0.15388,-0.98527,187.05,0.36173,0.91655,0.17052,154.34,0.9293,-0.36912,0.012664,293.07
> view matrix models
> #7,0.074549,0.15388,-0.98527,216.46,0.36173,0.91655,0.17052,179.38,0.9293,-0.36912,0.012664,250.38
> view matrix models
> #7,0.074549,0.15388,-0.98527,215.83,0.36173,0.91655,0.17052,189.39,0.9293,-0.36912,0.012664,271.22
> view matrix models
> #7,-0.55587,-0.42964,0.71163,248.69,0.65512,0.30053,0.69318,217.76,-0.51168,0.85152,0.11441,220.68
> view matrix models
> #7,-0.55354,-0.4312,0.7125,248.77,0.65869,0.29685,0.69138,217.89,-0.50963,0.85203,0.11971,220.73
> view matrix models
> #7,-0.55354,-0.4312,0.7125,239.53,0.65869,0.29685,0.69138,225.9,-0.50963,0.85203,0.11971,203.51
> fitmap #7 inMap #1
Fit molecule Cas23_AF-Q02ML8-F1-model_v4(1).pdb (#7) to map
cryosparc_P29_J1146_004_volume_map.mrc (#1) using 813 atoms
average map value = 0.5611, steps = 80
shifted from previous position = 8.71
rotated from previous position = 15.1 degrees
atoms outside contour = 401, contour level = 0.47644
Position of Cas23_AF-Q02ML8-F1-model_v4(1).pdb (#7) relative to
cryosparc_P29_J1146_004_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.63946677 -0.54430006 0.54297298 239.72210075
0.44931738 0.30849625 0.83841752 232.49791492
-0.62385585 0.78010735 0.04729038 204.84864096
Axis -0.03801985 0.76080479 0.64786616
Axis point 128.79331973 0.00000000 -73.65772833
Rotation angle (degrees) 129.92916667
Shift along axis 300.48583204
> volume #1 level 1.004
> view matrix models
> #7,-0.63947,-0.5443,0.54297,278.9,0.44932,0.3085,0.83842,219.39,-0.62386,0.78011,0.04729,258.15
> view matrix models
> #7,-0.59163,-0.44212,0.67417,274.75,0.17422,0.74635,0.64235,199.44,-0.78716,0.49749,-0.36454,264.35
> view matrix models
> #7,-0.59163,-0.44212,0.67417,240.53,0.17422,0.74635,0.64235,216.2,-0.78716,0.49749,-0.36454,212.25
> view matrix models
> #7,-0.59163,-0.44212,0.67417,241.91,0.17422,0.74635,0.64235,209.7,-0.78716,0.49749,-0.36454,203.96
> view matrix models
> #7,-0.59163,-0.44212,0.67417,240.15,0.17422,0.74635,0.64235,206.77,-0.78716,0.49749,-0.36454,207.53
> fitmap #7 inMap #1
Fit molecule Cas23_AF-Q02ML8-F1-model_v4(1).pdb (#7) to map
cryosparc_P29_J1146_004_volume_map.mrc (#1) using 813 atoms
average map value = 0.8088, steps = 144
shifted from previous position = 4.94
rotated from previous position = 28.7 degrees
atoms outside contour = 505, contour level = 1.0041
Position of Cas23_AF-Q02ML8-F1-model_v4(1).pdb (#7) relative to
cryosparc_P29_J1146_004_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.42425645 -0.13738786 0.89505922 233.97834000
0.14152151 0.96621848 0.21539145 195.21754806
-0.89441495 0.21805135 -0.39048109 212.52259052
Axis 0.00146868 0.98806951 0.15400158
Axis point 174.02458884 0.00000000 15.87511737
Rotation angle (degrees) 115.10380342
Shift along axis 225.96096147
> open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/AlphaFold/Cas23_AF-Q02ML8-F1-model_v4(1).pdb
Cas23_AF-Q02ML8-F1-model_v4(1).pdb title:
Alphafold monomer V2.0 prediction for crispr-associated nuclease/helicase CAS3
subtype I-F/ypest (Q02ML8) [more info...]
Chain information for Cas23_AF-Q02ML8-F1-model_v4(1).pdb #8
---
Chain | Description | UniProt
A | crispr-associated nuclease/helicase CAS3 subtype I-F/ypest | CAS3_PSEAB
1-1076
> select add #8
9350 atoms, 9560 bonds, 1176 residues, 2 models selected
> view matrix models
> #7,-0.81252,0.37493,-0.44637,201.47,0.57903,0.60754,-0.5437,15.854,0.06734,-0.70023,-0.71074,-43.863,#8,-0.10632,0.15113,0.98278,-11.422,-0.81577,0.55186,-0.17311,141.15,-0.56852,-0.82013,0.064613,237.3
> undo
> select subtract #7
8537 atoms, 8736 bonds, 1076 residues, 1 model selected
> view matrix models #8,1,0,0,355.28,0,1,0,124.25,0,0,1,42.922
> delete #7:101-1076
> delete #8:101-1076
> view matrix models
> #8,0.98989,0.075498,0.12008,357.46,-0.13733,0.72196,0.67816,135.57,-0.035495,-0.6878,0.72503,57.966
> view matrix models
> #8,0.98989,0.075498,0.12008,287.24,-0.13733,0.72196,0.67816,325.66,-0.035495,-0.6878,0.72503,304.16
> view matrix models
> #8,0.98989,0.075498,0.12008,262.23,-0.13733,0.72196,0.67816,305.33,-0.035495,-0.6878,0.72503,313.67
> view matrix models
> #8,0.98989,0.075498,0.12008,270.18,-0.13733,0.72196,0.67816,246.48,-0.035495,-0.6878,0.72503,292.12
> view matrix models
> #8,0.98989,0.075498,0.12008,255.87,-0.13733,0.72196,0.67816,230.49,-0.035495,-0.6878,0.72503,287.9
> volume #1 level 0.9635
> view matrix models
> #8,0.98357,-0.10268,-0.14849,258.77,0.048472,-0.64213,0.76506,277.96,-0.17391,-0.75969,-0.6266,274.42
> view matrix models
> #8,0.98357,-0.10268,-0.14849,278.89,0.048472,-0.64213,0.76506,327,-0.17391,-0.75969,-0.6266,267.55
> view matrix models
> #8,0.91327,0.21512,-0.34591,264.21,-0.34397,-0.047637,-0.93777,287.03,-0.21821,0.97542,0.030489,212.86
> view matrix models
> #8,0.69044,0.012687,-0.72328,250.12,-0.72069,0.098384,-0.68624,246.08,0.062452,0.99507,0.077072,238.86
> view matrix models
> #8,0.69944,-0.062361,-0.71197,252.79,-0.69284,-0.30363,-0.65405,259.93,-0.17539,0.95075,-0.25557,234.82
> view matrix models
> #8,0.69944,-0.062361,-0.71197,236.29,-0.69284,-0.30363,-0.65405,258.53,-0.17539,0.95075,-0.25557,204.83
> view matrix models
> #8,0.69944,-0.062361,-0.71197,236.99,-0.69284,-0.30363,-0.65405,231.01,-0.17539,0.95075,-0.25557,205.69
> fitmap #8 inMap #1
Fit molecule Cas23_AF-Q02ML8-F1-model_v4(1).pdb (#8) to map
cryosparc_P29_J1146_004_volume_map.mrc (#1) using 813 atoms
average map value = 0.6215, steps = 100
shifted from previous position = 4.58
rotated from previous position = 13 degrees
atoms outside contour = 587, contour level = 0.96348
Position of Cas23_AF-Q02ML8-F1-model_v4(1).pdb (#8) relative to
cryosparc_P29_J1146_004_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.70342590 0.11685940 -0.70109619 228.84717140
-0.60071263 -0.42949624 -0.67429763 235.67076865
-0.37991620 0.89547577 -0.23191986 202.06924277
Axis 0.89413419 -0.18294234 -0.40872504
Axis point 0.00000000 63.47511632 236.35000940
Rotation angle (degrees) 118.61979141
Shift along axis 78.91516019
> view matrix models
> #8,-0.59938,-0.41434,0.68489,256.74,-0.57062,-0.37888,-0.72859,232.05,0.56137,-0.82751,-0.009343,269.05
> view matrix models
> #8,-0.59938,-0.41434,0.68489,242,-0.57062,-0.37888,-0.72859,239.78,0.56137,-0.82751,-0.009343,275.08
> fitmap #8 inMap #1
Fit molecule Cas23_AF-Q02ML8-F1-model_v4(1).pdb (#8) to map
cryosparc_P29_J1146_004_volume_map.mrc (#1) using 813 atoms
average map value = 0.6077, steps = 132
shifted from previous position = 3.45
rotated from previous position = 46.6 degrees
atoms outside contour = 598, contour level = 0.96348
Position of Cas23_AF-Q02ML8-F1-model_v4(1).pdb (#8) relative to
cryosparc_P29_J1146_004_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.69909368 -0.31873259 0.64006058 232.05344732
-0.71293509 0.37918891 -0.58986380 212.74598371
-0.05469505 -0.86869172 -0.49232422 259.36647365
Axis -0.32955850 0.82116104 -0.46592461
Axis point 192.34270229 0.00000000 159.68800257
Rotation angle (degrees) 154.97380892
Shift along axis -22.62169354
> undo
[Repeated 1 time(s)]
> open 8lfj
Fetching url http://files.rcsb.org/download/8lfj.cif failed:
HTTP Error 404: Not Found
> open 8flj
Summary of feedback from opening 8flj fetched from pdb
---
warnings | Atom H1 is not in the residue template for GLY /F:1
Atom H1 is not in the residue template for GLY /H:1
Atom H1 is not in the residue template for MET /M:1
Atom H1 is not in the residue template for MET /N:1
8flj title:
Cas1-Cas2/3 integrase and IHF bound to CRISPR leader, repeat and foreign DNA
[more info...]
Chain information for 8flj #9
---
Chain | Description | UniProt
A B C D | CRISPR-associated endonuclease Cas1 | CAS1_PSEAB 1-324
E G | Integration host factor subunit alpha | IHFA_PSEAB 3-102
F H | Integration host factor subunit beta | IHFB_PSEAB 3-96
I | CRISPR leader, sense strand of DNA |
J | CRISPR leader and repeat, anti-sense strand of DNA |
K | CRISPR repeat and prespacer, sense strand of DNA |
L | Prespacer, anti-sense strand of DNA |
M N | CRISPR-associated nuclease/helicase Cas3 subtype I-F/YPEST | CAS3_PSEAB
1-1076
> select subtract #8
Nothing selected
> select add #9
57091 atoms, 58374 bonds, 431 pseudobonds, 3899 residues, 3 models selected
> view matrix models #9,1,0,0,10.086,0,1,0,8.1612,0,0,1,47.68
> view matrix models
> #9,0.97309,-0.079436,0.2163,-12.334,-0.0044558,0.93204,0.36234,-50.894,-0.23038,-0.35355,0.9066,185.43
> view matrix models
> #9,0.86495,0.16801,0.4729,-98.062,-0.34567,0.88258,0.31869,31.984,-0.36383,-0.43912,0.82146,246.03
> view matrix models
> #9,0.86495,0.16801,0.4729,-82.561,-0.34567,0.88258,0.31869,57.546,-0.36383,-0.43912,0.82146,241.76
> fitmap #9 inMap #1
Fit molecule 8flj (#9) to map cryosparc_P29_J1146_004_volume_map.mrc (#1)
using 57091 atoms
average map value = 0.4088, steps = 244
shifted from previous position = 7.62
rotated from previous position = 34.6 degrees
atoms outside contour = 47993, contour level = 0.96348
Position of 8flj (#9) relative to cryosparc_P29_J1146_004_volume_map.mrc (#1)
coordinates:
Matrix rotation and translation
0.93168204 0.35290639 -0.08617224 -26.89539314
-0.29648263 0.87575233 0.38099333 40.46783157
0.20992052 -0.32941607 0.92055333 73.93015512
Axis -0.70546779 -0.29403313 -0.64487186
Axis point 0.00000000 151.12150952 -25.60001576
Rotation angle (degrees) 30.23198656
Shift along axis -40.60052638
> delete #9/A-H
> delete #9/M-N
> delete #9/I-J
> volume #1 level 0.4277
> volume #1 level 0.8336
> delete #9/D:23-27
> delete #9/L:23-27
> delete #9/K:28-36
> volume #1 level 1.061
> volume #1 level 0.9554
> volume #1 level 1.053
> select add #8
2368 atoms, 2499 bonds, 53 pseudobonds, 149 residues, 3 models selected
> view matrix models
> #8,0.31658,0.20006,-0.92723,221.87,-0.79506,-0.47718,-0.37441,230.79,-0.51736,0.85573,0.0079911,200.37,#9,0.78891,0.53178,0.30795,-110.56,-0.61373,0.70708,0.35125,143.35,-0.030956,-0.4661,0.88419,158.29
> undo
> select subtract #9
813 atoms, 824 bonds, 100 residues, 1 model selected
> view matrix models
> #8,-0.66501,-0.017554,0.74663,243.79,-0.026593,-0.99853,-0.047163,264.24,0.74636,-0.051219,0.66357,252.21
> view matrix models
> #8,-0.68326,0.0078176,0.73013,228.9,-0.089007,-0.99338,-0.072657,257.92,0.72473,-0.11463,0.67943,258.64
> view matrix models
> #8,-0.67709,0.024143,0.7355,227.65,-0.18622,-0.97255,-0.1395,269.62,0.71195,-0.23142,0.66301,264.95
> view matrix models
> #8,-0.67709,0.024143,0.7355,225.8,-0.18622,-0.97255,-0.1395,263.7,0.71195,-0.23142,0.66301,271.14
> view matrix models
> #8,-0.67709,0.024143,0.7355,226.44,-0.18622,-0.97255,-0.1395,265.78,0.71195,-0.23142,0.66301,270.11
> fitmap #8 inMap #1
Fit molecule Cas23_AF-Q02ML8-F1-model_v4(1).pdb (#8) to map
cryosparc_P29_J1146_004_volume_map.mrc (#1) using 813 atoms
average map value = 0.8764, steps = 104
shifted from previous position = 2.92
rotated from previous position = 3.99 degrees
atoms outside contour = 508, contour level = 1.0528
Position of Cas23_AF-Q02ML8-F1-model_v4(1).pdb (#8) relative to
cryosparc_P29_J1146_004_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.62637450 0.04493003 0.77822637 221.29374102
-0.21241457 -0.97039596 -0.11494233 268.42329070
0.75002336 -0.23730356 0.61737508 272.75695868
Axis -0.42731979 0.09849286 -0.89871962
Axis point 57.78313995 145.65749080 0.00000000
Rotation angle (degrees) 171.76850940
Shift along axis -313.25744876
> view matrix models
> #8,-0.62637,0.04493,0.77823,236.34,-0.21241,-0.9704,-0.11494,267.24,0.75002,-0.2373,0.61738,282.01
> undo
> save /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/cryoem/cas1-2-3-prespacer-bound/isolde/chimeraXsessions/Alphafold-
> fragments-rigid-body-docked-local-refinement-J1446.cxs includeMaps true
——— End of log from Thu Apr 18 10:27:35 2024 ———
opened ChimeraX session
> open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/AlphaFold/Cas1-AF-Q02ML7-F1-model_v4.pdb
Cas1-AF-Q02ML7-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for crispr-associated endonuclease CAS1
(Q02ML7) [more info...]
Chain information for Cas1-AF-Q02ML7-F1-model_v4.pdb #10
---
Chain | Description | UniProt
A | crispr-associated endonuclease CAS1 | CAS1_PSEAB 1-324
> select subtract #8
Nothing selected
> select add #10
2549 atoms, 2602 bonds, 324 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #10,1,0,0,198.94,0,1,0,203.52,0,0,1,176.65
> view matrix models #10,1,0,0,265.8,0,1,0,213.72,0,0,1,179.36
> view matrix models #10,1,0,0,252.03,0,1,0,241.18,0,0,1,244.87
> mmaker #10 to #2
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 Cas1-AF-Q02ML7-F1-model_v4.pdb, chain A (#2) with
Cas1-AF-Q02ML7-F1-model_v4.pdb, chain A (#10), sequence alignment score =
1512.9
RMSD between 208 pruned atom pairs is 0.000 angstroms; (across all 208 pairs:
0.000)
> hide #4 models
> show #4 models
> hide #4 models
> open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/AlphaFold/Cas1-AF-Q02ML7-F1-model_v4.pdb
Cas1-AF-Q02ML7-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for crispr-associated endonuclease CAS1
(Q02ML7) [more info...]
Chain information for Cas1-AF-Q02ML7-F1-model_v4.pdb #11
---
Chain | Description | UniProt
A | crispr-associated endonuclease CAS1 | CAS1_PSEAB 1-324
> mmaker #11 to #3
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 Cas1-AF-Q02ML7-F1-model_v4.pdb, chain A (#3) with
Cas1-AF-Q02ML7-F1-model_v4.pdb, chain A (#11), sequence alignment score =
1512.9
RMSD between 208 pruned atom pairs is 0.000 angstroms; (across all 208 pairs:
0.000)
> hide #5 models
> close #4
> close #5
> combine #2-11
Remapping chain ID 'A' in Cas1-AF-Q02ML7-F1-model_v4.pdb #3 to 'B'
Remapping chain ID 'A' in Cas23_AF-Q02ML8-F1-model_v4(1).pdb #6 to 'C'
Remapping chain ID 'A' in Cas23_AF-Q02ML8-F1-model_v4(1).pdb #7 to 'D'
Remapping chain ID 'A' in Cas23_AF-Q02ML8-F1-model_v4(1).pdb #8 to 'E'
Remapping chain ID 'A' in Cas1-AF-Q02ML7-F1-model_v4.pdb #10 to 'F'
Remapping chain ID 'A' in Cas1-AF-Q02ML7-F1-model_v4.pdb #11 to 'G'
> close #6,8,10-11#7,9
> close #2-3
> save /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/cryoem/cas1-2-3-prespacer-
> bound/isolde/chimeraXsessions/20240510-Combined-model-fullCas1-rigid-body-
> docked-local-refinement-J1446-preisolde.cxs includeMaps true
——— End of log from Fri May 10 14:36:54 2024 ———
opened ChimeraX session
> select /A
1648 atoms, 1680 bonds, 208 residues, 1 model selected
> delete /A
> delete /B
> save /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/cryoem/cas1-2-3-prespacer-
> bound/isolde/chimeraXsessions/20240510-Combined-model-fullCas1-rigid-body-
> docked-local-refinement-J1446-preisolde.cxs includeMaps true
——— End of log from Fri May 10 14:39:35 2024 ———
opened ChimeraX session
> delete /G
> delete /K
> delete /L
> volume #1 level 0.8742
> save /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/cryoem/cas1-2-3-prespacer-
> bound/isolde/chimeraXsessions/20240513-Combined-model-fullactiveCas1-rigid-
> body-docked-local-refinement-J1446-preisolde.cxs
——— End of log from Mon May 13 09:07:39 2024 ———
opened ChimeraX session
> open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/cryoem/cas1-2-3-prespacer-
> bound/cryosparc/P6-P29/J1222/cryosparc_P29_J1222_004_volume_map_flipped.mrc
Opened cryosparc_P29_J1222_004_volume_map_flipped.mrc as #2, grid size
270,270,270, pixel 1.67, shown at level 0.183, step 2, values float32
> volume #2 step 1
> volume #2 level 0.7123
> fitmap #2 inMap #1
Fit map cryosparc_P29_J1222_004_volume_map_flipped.mrc in map
cryosparc_P29_J1146_004_volume_map.mrc using 24860 points
correlation = 0.4849, correlation about mean = 0.03438, overlap = 6717
steps = 92, shift = 4.81, angle = 8.45 degrees
Position of cryosparc_P29_J1222_004_volume_map_flipped.mrc (#2) relative to
cryosparc_P29_J1146_004_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.99078184 0.12326781 0.05618185 -40.28888926
-0.12628777 0.99053354 0.05380252 22.97696732
-0.04901788 -0.06040164 0.99696985 24.71451371
Axis -0.38855842 0.35792251 -0.84906645
Axis point 149.08676763 328.86599271 0.00000000
Rotation angle (degrees) 8.45072592
Shift along axis 2.89429673
> ui mousemode right "rotate selected models"
> select add #2
2 models selected
> view matrix models
> #2,0.94116,-0.30121,0.15324,53.269,-0.13417,-0.74921,-0.6486,596.99,0.31017,0.58988,-0.74554,200.67
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.94116,-0.30121,0.15324,49.776,-0.13417,-0.74921,-0.6486,573.45,0.31017,0.58988,-0.74554,183.68
> fitmap #2 inMap #1
Fit map cryosparc_P29_J1222_004_volume_map_flipped.mrc in map
cryosparc_P29_J1146_004_volume_map.mrc using 24860 points
correlation = 0.9779, correlation about mean = 0.7695, overlap = 3.127e+04
steps = 100, shift = 4.85, angle = 10.1 degrees
Position of cryosparc_P29_J1222_004_volume_map_flipped.mrc (#2) relative to
cryosparc_P29_J1146_004_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.98520884 -0.15938181 0.06293644 22.29611148
-0.07723773 -0.74089102 -0.66716927 565.35920343
0.15296368 0.65243999 -0.74224267 200.09159786
Axis 0.99576247 -0.06793356 0.06198501
Axis point 0.00000000 245.33062833 206.85454464
Rotation angle (degrees) 138.50057942
Shift along axis -3.80255207
> close #1
> save /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/cryoem/cas1-2-3-prespacer-
> bound/isolde/chimeraXsessions/20240513-Combined-model-fullactiveCas1-rigid-
> body-docked-local-refinement-J1222-preisolde.cxs includeMaps true
——— End of log from Tue May 14 15:03:45 2024 ———
opened ChimeraX session
> fitmap #4 inMap #2
Fit molecule combination (#4) to map
cryosparc_P29_J1222_004_volume_map_flipped.mrc (#2) using 11899 atoms
average map value = 0.8188, steps = 36
shifted from previous position = 0.102
rotated from previous position = 0.0324 degrees
atoms outside contour = 5129, contour level = 0.71229
Position of combination (#4) relative to
cryosparc_P29_J1222_004_volume_map_flipped.mrc (#2) coordinates:
Matrix rotation and translation
0.24889894 -0.06066088 -0.96662794 226.23236814
-0.96847296 -0.02636752 -0.24771932 190.13611095
-0.01046071 0.99781010 -0.06531127 190.41076951
Axis 0.68671160 -0.52717432 -0.50051414
Axis point 0.00000000 102.79259396 256.13801666
Rotation angle (degrees) 114.92237048
Shift along axis -40.18176579
> select add #2
2 models selected
> save /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/cryoem/cas1-2-3-prespacer-
> bound/isolde/chimeraXsessions/20240514-Combined-model-fullactiveCas1-rigid-
> body-docked-local-refinement-J1222-preisolde.cxs includeMaps true
Taking snapshot of stepper: combination
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 1392, in take_snapshot
'structure state': Structure.take_snapshot(self, session, flags),
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 208, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 344, in take_snapshot
'positions': self.positions.array(),
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x151072d60> ->
<chimerax.atomic.structure.AtomicStructure object at 0x169a86400>
'combination'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'isolde residue stepper 0' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x151072d60> ->
<chimerax.atomic.structure.AtomicStructure object at 0x169a86400>
'combination': Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x151072d60> ->
<chimerax.atomic.structure.AtomicStructure object at 0x169a86400>
'combination'
ValueError: error processing: 'isolde residue stepper 0' -> -> 'combination':
Error while saving session data for 'isolde residue stepper 0' -> ->
'combination'
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 1392, in take_snapshot
'structure state': Structure.take_snapshot(self, session, flags),
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 208, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 344, in take_snapshot
'positions': self.positions.array(),
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x151072d60> ->
<chimerax.atomic.structure.AtomicStructure object at 0x169a86400>
'combination'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'isolde residue stepper 0' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x151072d60> ->
<chimerax.atomic.structure.AtomicStructure object at 0x169a86400>
'combination': Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x151072d60> ->
<chimerax.atomic.structure.AtomicStructure object at 0x169a86400>
'combination'
ValueError: error processing: 'isolde residue stepper 0' -> -> 'combination':
Error while saving session data for 'isolde residue stepper 0' -> ->
'combination'
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/cryoem/cas1-2-3-prespacer-
> bound/isolde/chimeraXsessions/20240514-Combined-model-fullactiveCas1-rigid-
> body-docked-local-refinement-J1222-preisolde.cxs includeMaps true
Taking snapshot of stepper: combination
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 1392, in take_snapshot
'structure state': Structure.take_snapshot(self, session, flags),
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 208, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 344, in take_snapshot
'positions': self.positions.array(),
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x151072d60> ->
<chimerax.atomic.structure.AtomicStructure object at 0x169a86400>
'combination'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'isolde residue stepper 0' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x151072d60> ->
<chimerax.atomic.structure.AtomicStructure object at 0x169a86400>
'combination': Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x151072d60> ->
<chimerax.atomic.structure.AtomicStructure object at 0x169a86400>
'combination'
ValueError: error processing: 'isolde residue stepper 0' -> -> 'combination':
Error while saving session data for 'isolde residue stepper 0' -> ->
'combination'
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 1392, in take_snapshot
'structure state': Structure.take_snapshot(self, session, flags),
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 208, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 344, in take_snapshot
'positions': self.positions.array(),
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x151072d60> ->
<chimerax.atomic.structure.AtomicStructure object at 0x169a86400>
'combination'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'isolde residue stepper 0' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x151072d60> ->
<chimerax.atomic.structure.AtomicStructure object at 0x169a86400>
'combination': Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x151072d60> ->
<chimerax.atomic.structure.AtomicStructure object at 0x169a86400>
'combination'
ValueError: error processing: 'isolde residue stepper 0' -> -> 'combination':
Error while saving session data for 'isolde residue stepper 0' -> ->
'combination'
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 86
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro17,1
Model Number: MJ123LL/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.1.1
OS Loader Version: 10151.1.1
Software:
System Software Overview:
System Version: macOS 14.0 (23A344)
Kernel Version: Darwin 23.0.0
Time since boot: 35 days, 3 hours, 57 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
LG QHD:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 75.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.21.0
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.6.0
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
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: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (1)
comment:1 by , 18 months ago
| Component: | Unassigned → Third Party |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → ISOLDE: ResidueStepper holding reference to closed structure |
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From 1.6.1, so probably already fixed.