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Opened 20 months ago
Closed 20 months ago
#14636 closed defect (fixed)
MatchMaker: cannot access local variable 'concise_model_spec'
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Comparison | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.5-arm64-arm-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/lp212/Dropbox (Cambridge University)/RAD51/Papers/Abasic DNA
> filament/CryoEM/Figure 2 - cryoem/RAD51-AP-dsDNA.cxs"
Opened 6asm_AR.mrc (3D refine map) as #6, grid size 200,200,200, pixel 1.3,
shown at level 0.012, step 1, values float32
Opened 6asm_AR.mrc zone around DNA as #7, grid size 200,200,200, pixel 1.3,
shown at level 0.012, step 1, values float32
Opened 6asm_AR.mrc zone around DNA (filled APs) as #8, grid size 200,200,200,
pixel 1.3, shown at level 0.0122, step 1, values float32
Log from Fri Feb 23 16:06:03 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/luca/Dropbox (Cambridge University)/RAD51/Papers/Abasic DNA
> filament/CryoEM/Figure 2 - cryoem/RAD51-AP-dsDNA.cxs"
Opened 6asm_AR.mrc (3D refine map) as #6, grid size 200,200,200, pixel 1.3,
shown at level 0.012, step 1, values float32
Opened 6asm_AR.mrc zone around DNA as #7, grid size 200,200,200, pixel 1.3,
shown at level 0.012, step 1, values float32
Opened 6asm_AR.mrc zone around DNA (filled APs) as #8, grid size 200,200,200,
pixel 1.3, shown at level 0.0122, step 1, values float32
Log from Fri Mar 3 18:07:51 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/luca/Dropbox (Cambridge University)/RAD51/Papers/Abasic DNA
> filament/CryoEM/Figure 2 - cryoem/RAD51-AP-dsDNA.cxs" format session
Opened 6asm_AR.mrc (3D refine map) as #6, grid size 200,200,200, pixel 1.3,
shown at level 0.012, step 1, values float32
Opened 6asm_AR.mrc zone around DNA as #7, grid size 200,200,200, pixel 1.3,
shown at level 0.012, step 1, values float32
Opened 6asm_AR.mrc zone around DNA (filled APs) as #8, grid size 200,200,200,
pixel 1.3, shown at level 0.0122, step 1, values float32
Log from Fri Mar 3 13:15:08 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/luca/Dropbox (Cambridge University)/RAD51/Papers/Abasic DNA
> filament/CryoEM/Figure 2 - cryoem/RAD51-AP-dsDNA.cxs" format session
Opened 6asm_AR.mrc as #1, grid size 200,200,200, pixel 1.3, shown at level
0.0129, step 1, values float32
Opened 20210506 RAD51 Postsynapsis 3DRefine.mrc as #2, grid size 204,204,204,
pixel 1.3, shown at level 0.0143, step 1, values float32
Opened 6asm_AR.mrc zone as #4, grid size 200,200,200, pixel 1.3, shown at
level 0.0129, step 1, values float32
Opened 20210506 RAD51 Postsynapsis 3DRefine.mrc zone as #5, grid size
204,204,204, pixel 1.3, shown at level 0.0126, step 1, values float32
Log from Wed Feb 1 10:34:19 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/luca/Dropbox (Cambridge University)/RAD51/Papers/Abasic DNA
> filament/CryoEM/RAD51-AP-DNA.cxs" format session
Opened 6asm_AR.mrc as #1, grid size 200,200,200, pixel 1.3, shown at level
0.0129, step 1, values float32
Opened 20210506 RAD51 Postsynapsis 3DRefine.mrc as #2, grid size 204,204,204,
pixel 1.3, shown at level 0.0143, step 1, values float32
Opened 6asm_AR.mrc zone as #4, grid size 200,200,200, pixel 1.3, shown at
level 0.0129, step 1, values float32
Opened 20210506 RAD51 Postsynapsis 3DRefine.mrc zone as #5, grid size
204,204,204, pixel 1.3, shown at level 0.0126, step 1, values float32
Log from Mon Jan 30 16:37:24 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/luca/Dropbox (Cambridge University)/RAD51/Papers/Abasic DNA
> filament/CryoEM/RAD51-AP-DNA.cxs"
Opened 6asm_AR.mrc as #1, grid size 200,200,200, pixel 1.3, shown at level
0.0129, step 1, values float32
Opened 20210506 RAD51 Postsynapsis 3DRefine.mrc as #2, grid size 204,204,204,
pixel 1.3, shown at level 0.0143, step 1, values float32
Opened 6asm_AR.mrc zone as #4, grid size 200,200,200, pixel 1.3, shown at
level 0.0129, step 1, values float32
Opened 20210506 RAD51 Postsynapsis 3DRefine.mrc zone as #5, grid size
204,204,204, pixel 1.3, shown at level 0.0126, step 1, values float32
Log from Fri Jan 27 17:26:28 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/luca/Dropbox (Cambridge University)/RAD51/Structures/Abasic-
> filament/maps/6asm_AR.mrc"
Opened 6asm_AR.mrc as #1, grid size 200,200,200, pixel 1.3, shown at level
0.012, step 1, values float32
> open "/Users/luca/Dropbox (Cambridge University)/RAD51/Structures/RAD51
> post-synaptic filament - Robert/20210506 RAD51 Postsynapsis 3DRefine.mrc"
Opened 20210506 RAD51 Postsynapsis 3DRefine.mrc as #2, grid size 204,204,204,
pixel 1.3, shown at level 0.00875, step 1, values float32
> select add #2
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.7196,-0.11602,0.68463,151.24,0.69327,-0.17594,0.69887,-26.349,0.039374,0.97754,0.20704,-31.068
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.7196,-0.11602,0.68463,149.46,0.69327,-0.17594,0.69887,-29.153,0.039374,0.97754,0.20704,-50.972
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.71856,-0.14837,0.67945,154.34,0.69016,-0.2726,0.67036,-12.005,0.085755,0.95062,0.29828,-65.57
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.71856,-0.14837,0.67945,150.88,0.69016,-0.2726,0.67036,-21.229,0.085755,0.95062,0.29828,-76.73
> select clear
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit map 20210506 RAD51 Postsynapsis 3DRefine.mrc in map 6asm_AR.mrc using
84803 points
correlation = 0.9005, correlation about mean = 0.518, overlap = 26.93
steps = 132, shift = 9.54, angle = 11.2 degrees
Position of 20210506 RAD51 Postsynapsis 3DRefine.mrc (#2) relative to
6asm_AR.mrc (#1) coordinates:
Matrix rotation and translation
-0.78024822 -0.03757540 0.62434029 156.60148064
0.58112413 -0.41271119 0.70140161 14.75618209
0.23131678 0.91008657 0.34385315 -101.87893386
Axis 0.27382658 0.51570695 0.81182840
Axis point 91.65696573 59.90936604 0.00000000
Rotation angle (degrees) 157.60106772
Shift along axis -32.21669819
> fitmap #2 inMap #1
Fit map 20210506 RAD51 Postsynapsis 3DRefine.mrc in map 6asm_AR.mrc using
84803 points
correlation = 0.9005, correlation about mean = 0.518, overlap = 26.93
steps = 44, shift = 0.0014, angle = 0.00538 degrees
Position of 20210506 RAD51 Postsynapsis 3DRefine.mrc (#2) relative to
6asm_AR.mrc (#1) coordinates:
Matrix rotation and translation
-0.78023183 -0.03748832 0.62436601 156.58325263
0.58112155 -0.41269596 0.70141270 14.75376108
0.23137855 0.91009706 0.34378380 -101.87941736
Axis 0.27385869 0.51572159 0.81180826
Axis point 91.65105560 59.90579176 0.00000000
Rotation angle (degrees) 157.60390403
Shift along axis -32.21603554
> fitmap #2 inMap #1
Fit map 20210506 RAD51 Postsynapsis 3DRefine.mrc in map 6asm_AR.mrc using
84803 points
correlation = 0.9005, correlation about mean = 0.5181, overlap = 26.94
steps = 44, shift = 0.0149, angle = 0.00641 degrees
Position of 20210506 RAD51 Postsynapsis 3DRefine.mrc (#2) relative to
6asm_AR.mrc (#1) coordinates:
Matrix rotation and translation
-0.78020042 -0.03739098 0.62441109 156.56511208
0.58112860 -0.41269765 0.70140587 14.75499824
0.23146674 0.91010030 0.34371585 -101.86892273
Axis 0.27390525 0.51572781 0.81178860
Axis point 91.64464203 59.89960115 0.00000000
Rotation angle (degrees) 157.60677874
Shift along axis -32.20246138
> fitmap #2 inMap #1
Fit map 20210506 RAD51 Postsynapsis 3DRefine.mrc in map 6asm_AR.mrc using
84803 points
correlation = 0.9005, correlation about mean = 0.5179, overlap = 26.93
steps = 44, shift = 0.0219, angle = 0.0153 degrees
Position of 20210506 RAD51 Postsynapsis 3DRefine.mrc (#2) relative to
6asm_AR.mrc (#1) coordinates:
Matrix rotation and translation
-0.78025411 -0.03763990 0.62432904 156.60907166
0.58114165 -0.41268866 0.70140035 14.75172906
0.23125288 0.91009412 0.34387614 -101.88067912
Axis 0.27380360 0.51571097 0.81183359
Axis point 91.65917451 59.91138869 0.00000000
Rotation angle (degrees) 157.59808832
Shift along axis -32.22240222
> fitmap #2 inMap #1
Fit map 20210506 RAD51 Postsynapsis 3DRefine.mrc in map 6asm_AR.mrc using
84803 points
correlation = 0.9005, correlation about mean = 0.518, overlap = 26.94
steps = 44, shift = 0.0257, angle = 0.0123 degrees
Position of 20210506 RAD51 Postsynapsis 3DRefine.mrc (#2) relative to
6asm_AR.mrc (#1) coordinates:
Matrix rotation and translation
-0.78022013 -0.03744635 0.62438314 156.58032211
0.58113951 -0.41262988 0.70143671 14.73949173
0.23137289 0.91012876 0.34370369 -101.85487094
Axis 0.27387080 0.51575531 0.81178275
Axis point 91.64932151 59.89359524 0.00000000
Rotation angle (degrees) 157.60407883
Shift along axis -32.19927831
> fitmap #2 inMap #1 metric correlation
Fit map 20210506 RAD51 Postsynapsis 3DRefine.mrc in map 6asm_AR.mrc using
84803 points
correlation = 0.9007, correlation about mean = 0.5195, overlap = 26.92
steps = 40, shift = 0.0498, angle = 0.0998 degrees
Position of 20210506 RAD51 Postsynapsis 3DRefine.mrc (#2) relative to
6asm_AR.mrc (#1) coordinates:
Matrix rotation and translation
-0.78053352 -0.03576152 0.62409016 156.47472691
0.58031652 -0.41258317 0.70214518 14.75076058
0.23237932 0.91021769 0.34278799 -101.91927258
Axis 0.27409211 0.51599729 0.81155426
Axis point 91.63745921 59.85587805 0.00000000
Rotation angle (degrees) 157.69315062
Shift along axis -32.21317958
> fitmap #2 inMap #1 metric correlation
Fit map 20210506 RAD51 Postsynapsis 3DRefine.mrc in map 6asm_AR.mrc using
84803 points
correlation = 0.9006, correlation about mean = 0.5195, overlap = 26.91
steps = 28, shift = 0.0138, angle = 0.00446 degrees
Position of 20210506 RAD51 Postsynapsis 3DRefine.mrc (#2) relative to
6asm_AR.mrc (#1) coordinates:
Matrix rotation and translation
-0.78053796 -0.03568812 0.62408881 156.46704918
0.58028419 -0.41260765 0.70215752 14.75018269
0.23244513 0.91020947 0.34276519 -101.93623393
Axis 0.27411056 0.51599452 0.81154978
Axis point 91.63767656 59.85705970 0.00000000
Rotation angle (degrees) 157.69705490
Shift along axis -32.22604432
> fitmap #2 inMap #1
Fit map 20210506 RAD51 Postsynapsis 3DRefine.mrc in map 6asm_AR.mrc using
84803 points
correlation = 0.9005, correlation about mean = 0.5181, overlap = 26.93
steps = 44, shift = 0.0495, angle = 0.109 degrees
Position of 20210506 RAD51 Postsynapsis 3DRefine.mrc (#2) relative to
6asm_AR.mrc (#1) coordinates:
Matrix rotation and translation
-0.78023977 -0.03753858 0.62435307 156.59432331
0.58111842 -0.41272964 0.70139548 14.75991649
0.23135963 0.91007972 0.34384244 -101.88554730
Axis 0.27384368 0.51570148 0.81182610
Axis point 91.65529058 59.91098168 0.00000000
Rotation angle (degrees) 157.60262405
Shift along axis -32.21926959
> lighting simple
> lighting soft
> transparency #2.1 50
> ui tool show "Side View"
> volume #1 level 0.0118
> transparency #2.1 0
> volume #2 level 0.01322
> volume #1 level 0.01537
> volume #2 level 0.01953
> select add #2
4 models selected
> transparency sel 50
> select subtract #2
Nothing selected
> volume #1 level 0.01688
> volume
> volume #1 surfaceSmoothing true
> volume #2 surfaceSmoothing true
> volume #1 subdivideSurface true
> volume #2 subdivideSurface true
> volume #1 level 0.01293
> volume #2 level 0.01585
> volume #2 level 0.01427
> open "/Users/luca/Dropbox (Cambridge University)/RAD51/Structures/RAD51-AP-
> DNA/coot/abasic_27.1.2023.pdb"
Summary of feedback from opening /Users/luca/Dropbox (Cambridge
University)/RAD51/Structures/RAD51-AP-DNA/coot/abasic_27.1.2023.pdb
---
warnings | Duplicate atom serial number found: 12201
Duplicate atom serial number found: 12202
Duplicate atom serial number found: 12203
Duplicate atom serial number found: 12204
Duplicate atom serial number found: 12205
24165 messages similar to the above omitted
Chain information for abasic_27.1.2023.pdb #3
---
Chain | Description
A B C D E F G H I J K | No description available
L | No description available
M | No description available
> show cartoons
> hide atoms
> show #!1 models
> hide #!2 models
> select /M:21
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
572 atoms, 636 bonds, 32 residues, 1 model selected
> select up
27789 atoms, 28301 bonds, 3518 residues, 1 model selected
> select down
572 atoms, 636 bonds, 32 residues, 1 model selected
> hide sel cartoons
> show sel atoms
> style sel sphere
Changed 572 atom styles
> style sel stick
Changed 572 atom styles
> color sel byhetero
> select /L:12
19 atoms, 20 bonds, 1 residue, 1 model selected
> select up
630 atoms, 704 bonds, 32 residues, 1 model selected
> select up
27789 atoms, 28301 bonds, 3518 residues, 1 model selected
> select down
630 atoms, 704 bonds, 32 residues, 1 model selected
> hide sel cartoons
> show sel atoms
> style sel stick
Changed 630 atom styles
> color sel byhetero
> transparency #1.1 50
> ui tool show "Model Panel"
> select clear
> volume zone nearAtoms #3:L,M range 5 newMap true
Missing or invalid "volumes" argument: invalid density maps specifier
> volume zone #1 nearAtoms #3:L,M range 5 newMap true
no atoms specified for zone
> volume zone #1 nearAtoms #3/L-M range 5 newMap true
Opened 6asm_AR.mrc zone as #4, grid size 200,200,200, pixel 1.3, shown at step
1, values float32
> volume zone #1 nearAtoms #3/L-M range 4 newMap true
Opened 6asm_AR.mrc zone as #5, grid size 200,200,200, pixel 1.3, shown at step
1, values float32
> ui tool show "Model Panel"
> hide #!3 models
> volume zone #1 nearAtoms #3/L-M range 3 newMap true
Opened 6asm_AR.mrc zone as #6, grid size 200,200,200, pixel 1.3, shown at step
1, values float32
> hide #!5 models
> volume #6 level 0.01142
> show #!3 models
> hide #!3 models
> show #!3 models
> open "/Users/luca/Dropbox (Cambridge University)/RAD51/Structures/RAD51
> post-synaptic filament - Robert/Final
> coords/post_RAD51dsDNA_10_real_space_refined_026-coot-3.pdb"
Chain information for post_RAD51dsDNA_10_real_space_refined_026-coot-3.pdb #7
---
Chain | Description
A B C D E F | No description available
G | No description available
H | No description available
> hide atoms
> show cartoons
> ui tool show Matchmaker
> matchmaker #7/C to #3/C pairing ss
Parameters
---
Chain pairing | ss
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 abasic_27.1.2023.pdb, chain C (#3) with
post_RAD51dsDNA_10_real_space_refined_026-coot-3.pdb, chain C (#7), sequence
alignment score = 1577.4
RMSD between 311 pruned atom pairs is 0.304 angstroms; (across all 311 pairs:
0.304)
> matchmaker #7/C to #3/C pairing ss
Parameters
---
Chain pairing | ss
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 abasic_27.1.2023.pdb, chain C (#3) with
post_RAD51dsDNA_10_real_space_refined_026-coot-3.pdb, chain C (#7), sequence
alignment score = 1577.4
RMSD between 311 pruned atom pairs is 0.304 angstroms; (across all 311 pairs:
0.304)
> hide #!7 models
> hide #!6 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!7 models
> select #7/G:15
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
414 atoms, 464 bonds, 20 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 414 atom styles
> select #7/G:16
19 atoms, 20 bonds, 1 residue, 1 model selected
> select up
414 atoms, 464 bonds, 20 residues, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> style sel stick
Changed 414 atom styles
> hide #!3 models
> show #!3 models
> hide #!7 models
> select #3/M:20
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
572 atoms, 636 bonds, 32 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> show #!7 models
> select #7/G:16
19 atoms, 20 bonds, 1 residue, 1 model selected
> select up
414 atoms, 464 bonds, 20 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> hide #!7 models
> show #!7 models
> select clear
> select #7/H:8
19 atoms, 20 bonds, 1 residue, 1 model selected
> select up
406 atoms, 454 bonds, 20 residues, 1 model selected
> select add #3/L:15
425 atoms, 474 bonds, 21 residues, 2 models selected
> select up
1036 atoms, 1158 bonds, 52 residues, 2 models selected
> show sel atoms
> hide sel cartoons
> style sel stick
Changed 1036 atom styles
> select clear
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TYR"::name="VAL"
40528 atoms, 41106 bonds, 17 pseudobonds, 5287 residues, 4 models selected
> hide sel cartoons
> select #7/G:12@C2'
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 20 bonds, 1 residue, 1 model selected
> select up
414 atoms, 464 bonds, 20 residues, 1 model selected
> color sel byhetero
> select clear
> hide #!3 models
> select #7/H:8@C2'
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 20 bonds, 1 residue, 1 model selected
> select up
406 atoms, 454 bonds, 20 residues, 1 model selected
> color sel byhetero
> select clear
> volume zone #1 nearAtoms #7/G-H range 3 newMap true
Opened 6asm_AR.mrc zone as #8, grid size 200,200,200, pixel 1.3, shown at step
1, values float32
> show #!6 models
> hide #!8 models
> hide #!7 models
> show #!5 models
> show #!4 models
> close #5
> show #!8 models
> close #6
> close #4
> volume #8 level 0.01345
> volume #8 level 0.009995
> volume #8 level 0.01199
> volume zone #1 nearAtoms #7/G-H range 2 newMap true
Opened 6asm_AR.mrc zone as #4, grid size 200,200,200, pixel 1.3, shown at step
1, values float32
> hide #!4 models
> hide #!8 models
> show #!8 models
> show #!4 models
> hide #!8 models
> show #!8 models
> close #8
> close #4
> volume zone #1 nearAtoms #7/G-H range 2 newMap true
Opened 6asm_AR.mrc zone as #4, grid size 200,200,200, pixel 1.3, shown at step
1, values float32
> volume zone #2 nearAtoms #7/G-H range 2 newMap true
Opened 20210506 RAD51 Postsynapsis 3DRefine.mrc zone as #5, grid size
204,204,204, pixel 1.3, shown at step 1, values float32
> lighting simple
> lighting soft
> lighting simple
> lighting full
> set bgColor white
> graphics silhouettes true
> lighting simple
> lighting soft
> lighting full
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> volume #5 level 0.01263
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> graphics silhouettes false
> lighting simple
> lighting soft
> lighting full
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> select add #5
2 models selected
> transparency sel 50
> select subtract #5
Nothing selected
> save "/Users/luca/Dropbox (Cambridge University)/RAD51/Papers/Abasic DNA
> filament/CryoEM/map_superposition_ap-post.png" width 2270 height 2400
> supersample 3 transparentBackground true
> save "/Users/luca/Dropbox (Cambridge University)/RAD51/Papers/Abasic DNA
> filament/CryoEM/RAD51-AP-DNA.cxs"
——— End of log from Fri Jan 27 17:26:28 2023 ———
opened ChimeraX session
> view name view1
> view list
Named views: view1
> save "/Users/luca/Dropbox (Cambridge University)/RAD51/Papers/Abasic DNA
> filament/CryoEM/RAD51-AP-DNA.cxs"
> hide #!4 models
> hide #!5 models
> show #!3 models
> show #!7 models
> ui tool show "Side View"
> show atoms
> show cartoons
> hide atoms
> hide #!7 models
> dssp #3
> select #3/L:13
19 atoms, 20 bonds, 1 residue, 1 model selected
> select up
630 atoms, 704 bonds, 32 residues, 1 model selected
> select add #3/M:17
652 atoms, 728 bonds, 33 residues, 1 model selected
> select up
1202 atoms, 1340 bonds, 64 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 1202 atom styles
> hide sel cartoons
> select clear
> ~pseudobonds
Unknown command: ~pseudobonds
> ~pseudobond
Unknown command: ~pseudobond
> select pbonds
32 pseudobonds, 2 models selected
> hide sel
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> graphics silhouettes false
> lighting simple
> lighting soft
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TYR"::name="VAL"
40528 atoms, 41106 bonds, 17 pseudobonds, 5287 residues, 4 models selected
> hide sel & #!3 cartoons
> show sel & #!3 atoms
> select clear
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TYR"::name="VAL"
40528 atoms, 41106 bonds, 17 pseudobonds, 5287 residues, 4 models selected
> show sel & #!3 cartoons
> hide sel & #!3 atoms
> select clear
> select #3/C:283
7 atoms, 7 bonds, 1 residue, 1 model selected
> select add #3/C:285
16 atoms, 15 bonds, 2 residues, 1 model selected
> select add #3/C:284
25 atoms, 23 bonds, 3 residues, 1 model selected
> select add #3/C:286
32 atoms, 30 bonds, 4 residues, 1 model selected
> select add #3/C:273
39 atoms, 36 bonds, 5 residues, 1 model selected
> select up
56 atoms, 56 bonds, 7 residues, 1 model selected
> select add #3/C:271
61 atoms, 60 bonds, 8 residues, 1 model selected
> select up
75 atoms, 75 bonds, 10 residues, 1 model selected
> select #3/*:269-286
825 atoms, 825 bonds, 11 pseudobonds, 110 residues, 2 models selected
> ui tool show "Color Actions"
> color sel lime target c
> color sel spring green target c
> color sel lawn green target c
> color sel chartreuse target c
> color sel lime target c
> color sel medium spring green target c
> select clear
> select #3/*:269-286
825 atoms, 825 bonds, 11 pseudobonds, 110 residues, 2 models selected
> color sel chartreuse target c
> select clear
> select #3/*:269-286
825 atoms, 825 bonds, 11 pseudobonds, 110 residues, 2 models selected
> color sel lime target c
> select clear
> select #3/*:269-286
825 atoms, 825 bonds, 11 pseudobonds, 110 residues, 2 models selected
> color sel spring green target c
> color sel cyan target c
> select clear
> graphics silhouettes true
> select #3/M:17@N7
1 atom, 1 residue, 1 model selected
> select up
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
572 atoms, 636 bonds, 32 residues, 1 model selected
> color sel white target a
> select #3/L:15@C5
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 20 bonds, 1 residue, 1 model selected
> select up
630 atoms, 704 bonds, 32 residues, 1 model selected
> color sel khaki target a
> color sel wheat target a
> select clear
> select purines
135 atoms, 150 bonds, 15 residues, 2 models selected
> color sel lavender target a
[Repeated 2 time(s)]
> color sel yellow target a
[Repeated 1 time(s)]
> select pyrimidines
312 atoms, 312 bonds, 52 residues, 2 models selected
> color sel yellow target a
> select up
1006 atoms, 1077 bonds, 52 residues, 2 models selected
> select down
312 atoms, 312 bonds, 52 residues, 2 models selected
> select purines
513 atoms, 570 bonds, 57 residues, 2 models selected
> color sel cornflower blue target a
> select #3/M:18@C3'
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
572 atoms, 636 bonds, 32 residues, 1 model selected
> color sel white target a
> select #3/L:15@C5
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 20 bonds, 1 residue, 1 model selected
> select up
630 atoms, 704 bonds, 32 residues, 1 model selected
> color sel wheat target a
> color sel dark khaki target a
> select clear
> select ::name="3DR"
110 atoms, 110 bonds, 10 residues, 1 model selected
> color sel lavender target a
> color sel plum target a
> color sel violet target a
> color sel lavender target a
> color sel light cyan target a
> color sel plum target a
> select clear
> save "/Users/luca/Dropbox (Cambridge University)/RAD51/Papers/Abasic DNA
> filament/CryoEM/RAD51-AP-DNA.cxs"
[Repeated 1 time(s)]
——— End of log from Mon Jan 30 16:37:24 2023 ———
opened ChimeraX session
> ui tool show "Model Panel"
> save "/Users/luca/Dropbox (Cambridge University)/RAD51/Papers/Abasic DNA
> filament/CryoEM/RAD51-AP-DNA.cxs"
——— End of log from Wed Feb 1 10:34:19 2023 ———
opened ChimeraX session
> open "/Users/luca/Dropbox (Cambridge University)/RAD51/Structures/RAD51-AP-
> dsDNA/phenix/RealSpaceRefine_2/APdsDNA_02.03_real_space_refined_002.pdb"
Chain information for APdsDNA_02.03_real_space_refined_002.pdb #6
---
Chain | Description
A B C D E F I | No description available
L | No description available
M | No description available
> close #3
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> close #7
> select intersect protein
Nothing selected
> hide atoms
> show cartoons
> ui tool show "Color Actions"
> color light sky blue target c
> color light steel blue target c
> select intersect nucleic-acid
Nothing selected
> show atoms
> undo
> select clear
> select intersect nucleic-acid
Nothing selected
> show atoms
> undo
> select nucleic-acid
866 atoms, 965 bonds, 46 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> select clear
> select phosphate
311 atoms, 260 bonds, 53 residues, 1 model selected
> color sel red
> select ribose
368 atoms, 368 bonds, 46 residues, 1 model selected
> color sel orange red target a
> color sel orange target a
> select clear
> select adenine|cytosine|guanine|thymine|uracil
430 atoms, 453 bonds, 46 residues, 1 model selected
> color sel khaki target a
> select clear
> lighting simple
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting full
> lighting soft
> lighting full
> lighting soft
> select /M:4@OP1
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select add /M:4@P
2 atoms, 1 residue, 1 model selected
> select add /M:4@OP2
3 atoms, 1 residue, 1 model selected
> color sel red target a
> select clear
> select /L:17@P
1 atom, 1 residue, 1 model selected
> select up
21 atoms, 23 bonds, 1 residue, 1 model selected
> select up
453 atoms, 506 bonds, 23 residues, 1 model selected
> color sel rosy brown target a
> color sel tan target a
> color sel rosy brown target a
> color sel dark gray target a
> color sel rosy brown target a
> color sel burly wood target a
> color sel rosy brown target a
> color sel dark khaki target a
> color sel peru target a
> color sel dark goldenrod target a
> color sel rosy brown target a
> select clear
> camera mono
> camera ortho
> camera mono
> ui tool show "Side View"
> graphics silhouettes false
> view list
Named views: view1
> view name view1
> save "/Users/luca/Dropbox (Cambridge University)/RAD51/Papers/Abasic DNA
> filament/CryoEM/Figure 2 - cryoem/RAD51-AP-dsDNA.png" width 3237 height 2400
> supersample 3
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> open "/Users/luca/Dropbox (Cambridge University)/RAD51/Structures/RAD51-AP-
> dsDNA/Abasic-filament-
> old/Phenix/LocalAnisoSharpen_2/run_half1_class001_unfil_and_run_half2_class001_unfil_sharpened.ccp4"
Opened run_half1_class001_unfil_and_run_half2_class001_unfil_sharpened.ccp4 as
#3, grid size 200,200,200, pixel 1.3, shown at level 0.0144, step 1, values
float32
> ui tool show "Color Zone"
> volume zone #6/M,L range 3 newMap true
Missing required "near_atoms" argument
> volume zone #3 nearAtoms 6/M,L range 3 newMap true
Invalid "nearAtoms" argument: invalid atoms specifier
> volume zone #3 nearAtoms #6/M,L range 3 newMap true
Opened run_half1_class001_unfil_and_run_half2_class001_unfil_sharpened.ccp4
zone as #7, grid size 200,200,200, pixel 1.3, shown at step 1, values float32
> hide #!7 models
> show #!7 models
> hide #!6 models
> graphics silhouettes true
> volume #4 level 0.009926
> hide #!4 models
> volume #4 level 0.01003
> volume #4 level 0.009926
> volume #7 level 0.0179
> volume zone #3 nearAtoms #6/M,L range 2 newMap true
Opened run_half1_class001_unfil_and_run_half2_class001_unfil_sharpened.ccp4
zone as #8, grid size 200,200,200, pixel 1.3, shown at step 1, values float32
> close #7
> volume #8 level 0.01187
> volume #8 level 0.0158
> show #!5 models
> hide #!8 models
> volume #5 level 0.004923
> close #5
> show #!4 models
> volume #4 level 0.00649
> view view1
> hide #!4 models
> show #!8 models
> select nucleic-acid
866 atoms, 965 bonds, 46 residues, 1 model selected
> transparency #8.1 50
> show #!6 models
> nucleotides sel fill
> style nucleic & sel stick
Changed 866 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 866 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 866 atom styles
> select protein
16688 atoms, 16926 bonds, 7 pseudobonds, 2177 residues, 2 models selected
> hide sel cartoons
> select clear
[Repeated 1 time(s)]
> ui tool show "Side View"
> lighting simple
> lighting soft
> lighting full
> save "/Users/luca/Dropbox (Cambridge University)/RAD51/Papers/Abasic DNA
> filament/CryoEM/Figure 2 - cryoem/map_DNAonly.png" width 3237 height 2400
> supersample 3
> show #!2 models
> volume zone #2 nearAtoms #6/M,L range 2 newMap true
Opened 20210506 RAD51 Postsynapsis 3DRefine.mrc zone as #5, grid size
204,204,204, pixel 1.3, shown at step 1, values float32
> hide #!5 models
> show #!5 models
> volume #5 level 0.002473
> select add #8
2 models selected
> transparency sel 0
> select add #5
4 models selected
> select subtract #8
2 models selected
> transparency sel 50
> select clear
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> volume #5 level 0.01065
> show #!6 models
> hide #!8 models
> hide #!5 models
> show #!8 models
> show #!2 models
> view #8 clip false
> hide #!2 models
> hide #!8 models
> open "/Users/luca/Dropbox (Cambridge University)/RAD51/Structures/PDB
> deposition/post-NPF/coords/post-npf.pdb"
Chain information for post-npf.pdb #7
---
Chain | Description
A B C D E F | No description available
G | No description available
H | No description available
> hide atoms
> show cartoons
> ui tool show Matchmaker
> matchmaker #!7 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 APdsDNA_02.03_real_space_refined_002.pdb, chain B (#6) with post-
npf.pdb, chain A (#7), sequence alignment score = 1597.2
RMSD between 311 pruned atom pairs is 0.403 angstroms; (across all 311 pairs:
0.403)
> select add #7
15442 atoms, 15624 bonds, 6 pseudobonds, 2044 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.63715,0.13206,-0.75934,131.62,-0.73631,0.39544,-0.54906,248.57,0.22777,0.90895,0.34919,-88.756
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.94969,-0.050481,0.3091,234.12,0.30771,-0.33426,0.89083,24.014,0.05835,0.94113,0.33298,-68.259
> ui tool show Matchmaker
> matchmaker #!7 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 APdsDNA_02.03_real_space_refined_002.pdb, chain B (#6) with post-
npf.pdb, chain A (#7), sequence alignment score = 1597.2
RMSD between 311 pruned atom pairs is 0.403 angstroms; (across all 311 pairs:
0.403)
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.63715,0.13206,-0.75934,140.1,-0.73631,0.39544,-0.54906,255.9,0.22777,0.90895,0.34919,-82.232
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.99548,-0.019416,0.092967,272.48,0.086293,-0.59376,0.8,110.3,0.039667,0.80441,0.59275,-73.428
> view matrix models
> #7,-0.96706,0.15584,0.20126,229.48,0.099424,-0.4966,0.86227,86.536,0.23432,0.85387,0.46475,-90.272
> view matrix models
> #7,-0.90731,0.39992,-0.12982,229.52,-0.31016,-0.42813,0.84883,134.07,0.28388,0.81041,0.51249,-96.989
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.90731,0.39992,-0.12982,211.85,-0.31016,-0.42813,0.84883,124.28,0.28388,0.81041,0.51249,-102.97
> select clear
> ui tool show Matchmaker
> matchmaker #7/D to #6/C pairing ss
Parameters
---
Chain pairing | ss
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 APdsDNA_02.03_real_space_refined_002.pdb, chain C (#6) with post-
npf.pdb, chain D (#7), sequence alignment score = 1563
RMSD between 311 pruned atom pairs is 0.402 angstroms; (across all 311 pairs:
0.402)
> matchmaker #7/D to #6/C pairing ss
Parameters
---
Chain pairing | ss
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 APdsDNA_02.03_real_space_refined_002.pdb, chain C (#6) with post-
npf.pdb, chain D (#7), sequence alignment score = 1563
RMSD between 311 pruned atom pairs is 0.402 angstroms; (across all 311 pairs:
0.402)
> select nucleic-acid
1686 atoms, 1883 bonds, 86 residues, 2 models selected
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 1686 atom styles
> hide sel cartoons
> select clear
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> select #7/G:20@C4'
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 20 bonds, 1 residue, 1 model selected
> select add #7/G:19@C4'
20 atoms, 20 bonds, 2 residues, 1 model selected
> select up
41 atoms, 45 bonds, 2 residues, 1 model selected
> select add #7/H:1@C2'
42 atoms, 45 bonds, 3 residues, 1 model selected
> select up
63 atoms, 69 bonds, 3 residues, 1 model selected
> select add #7/H:2@C4'
64 atoms, 69 bonds, 4 residues, 1 model selected
> select up
82 atoms, 90 bonds, 4 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #6/L:25@C3'
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 20 bonds, 1 residue, 1 model selected
> select add #6/L:26@C4'
20 atoms, 20 bonds, 2 residues, 1 model selected
> select up
40 atoms, 44 bonds, 2 residues, 1 model selected
> close #6
> open "/Users/luca/Dropbox (Cambridge University)/RAD51/Structures/RAD51-AP-
> dsDNA/coot/APdsDNA_02.03.2023.pdb"
Summary of feedback from opening /Users/luca/Dropbox (Cambridge
University)/RAD51/Structures/RAD51-AP-dsDNA/coot/APdsDNA_02.03.2023.pdb
---
warnings | Duplicate atom serial number found: 12201
Duplicate atom serial number found: 12202
Duplicate atom serial number found: 12203
Duplicate atom serial number found: 12204
Duplicate atom serial number found: 12205
14497 messages similar to the above omitted
Chain information for APdsDNA_02.03.2023.pdb #6
---
Chain | Description
A B C D E F I | No description available
L | No description available
M | No description available
> hide atoms
> show cartoons
> select nucleic-acid
1604 atoms, 1791 bonds, 82 residues, 2 models selected
> show sel atoms
> hide sel cartoons
> nucleotides sel atoms
> style nucleic & sel stick
Changed 1604 atom styles
> close #7
> open "/Users/luca/Dropbox (Cambridge University)/RAD51/Structures/PDB
> deposition/post-NPF/coords/post-npf.pdb"
Chain information for post-npf.pdb #7
---
Chain | Description
A B C D E F | No description available
G | No description available
H | No description available
> hide sel atoms
> show sel cartoons
> hide sel atoms
> show sel cartoons
> select clear
> select add #7
15442 atoms, 15624 bonds, 6 pseudobonds, 2044 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> ui mousemode right "translate selected models"
> view matrix models #7,1,0,0,-85.997,0,1,0,10.109,0,0,1,-0.80684
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.50715,-0.5745,0.64246,117.12,0.72801,-0.68454,-0.037437,157.05,0.46129,0.44873,0.76541,-97.06
> view matrix models
> #7,-0.86975,0.49207,-0.037356,102.22,-0.2566,-0.38629,0.88597,127.95,0.42153,0.78016,0.46224,-99.633
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.86975,0.49207,-0.037356,82.215,-0.2566,-0.38629,0.88597,130.54,0.42153,0.78016,0.46224,-101.07
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.38225,0.40035,-0.83283,132.61,-0.87386,0.13639,0.46665,194.09,0.30042,0.90615,0.29772,-81.259
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.38225,0.40035,-0.83283,220.26,-0.87386,0.13639,0.46665,144.51,0.30042,0.90615,0.29772,-78.955
> view matrix models
> #7,-0.38225,0.40035,-0.83283,220.82,-0.87386,0.13639,0.46665,144.38,0.30042,0.90615,0.29772,-79.61
> view matrix models
> #7,-0.38225,0.40035,-0.83283,232.41,-0.87386,0.13639,0.46665,173.31,0.30042,0.90615,0.29772,-73.489
> view matrix models
> #7,-0.38225,0.40035,-0.83283,238.24,-0.87386,0.13639,0.46665,167.93,0.30042,0.90615,0.29772,-74.575
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.31119,0.44805,-0.8381,222.46,-0.89553,0.15693,0.41641,174.47,0.31809,0.88013,0.3524,-80.363
> view matrix models
> #7,-0.31043,0.4455,-0.83974,222.94,-0.90367,0.13582,0.40612,179.93,0.29498,0.88492,0.36042,-78.954
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.31043,0.4455,-0.83974,222.58,-0.90367,0.13582,0.40612,176.63,0.29498,0.88492,0.36042,-78.811
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.33992,0.35853,-0.86943,242.88,-0.9165,0.081015,0.39174,188.08,0.21088,0.93,0.30105,-66.126
> view matrix models
> #7,-0.40663,0.447,-0.79677,229.83,-0.86999,0.07676,0.48706,169.98,0.27888,0.89123,0.35767,-77.172
> ui tool show Matchmaker
> matchmaker #7/H to #6/L pairing ss matrix Nucleic
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 APdsDNA_02.03.2023.pdb, chain L (#6) with post-npf.pdb, chain H
(#7), sequence alignment score = 34.7
RMSD between 10 pruned atom pairs is 0.706 angstroms; (across all 19 pairs:
4.394)
> matchmaker #7/H to #6/L pairing ss matrix Nucleic
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 APdsDNA_02.03.2023.pdb, chain L (#6) with post-npf.pdb, chain H
(#7), sequence alignment score = 34.7
RMSD between 10 pruned atom pairs is 0.706 angstroms; (across all 19 pairs:
4.394)
> select clear
> select nucleic-acid
1686 atoms, 1883 bonds, 86 residues, 2 models selected
> hide sel cartoons
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 1686 atom styles
> ui tool show "Build Structure"
> build start nucleic #7 CACC type dna form B
> hide #!7 models
> show #!7 models
> select #7/I:3@P
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 20 bonds, 1 residue, 1 model selected
> select up
75 atoms, 83 bonds, 4 residues, 1 model selected
> select add #7/J:1@C6
76 atoms, 83 bonds, 5 residues, 1 model selected
> select up
94 atoms, 104 bonds, 5 residues, 1 model selected
> select up
158 atoms, 176 bonds, 8 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.64006,0.12593,-0.75793,122.78,-0.73433,0.39043,-0.55527,253.53,0.22599,0.91198,0.34238,-57.249
> undo
> ui mousemode right select
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.64006,0.12593,-0.75793,124.57,-0.73433,0.39043,-0.55527,252.45,0.22599,0.91198,0.34238,-55.565
> undo
> ui mousemode right select
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.64006,0.12593,-0.75793,127.56,-0.73433,0.39043,-0.55527,250.61,0.22599,0.91198,0.34238,-54.645
> undo
> select clear
> select #7/I:1@C3'
1 atom, 1 residue, 1 model selected
> select up
16 atoms, 17 bonds, 1 residue, 1 model selected
> ui mousemode right select
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.64006,0.12593,-0.75793,120.79,-0.73433,0.39043,-0.55527,251.45,0.22599,0.91198,0.34238,-53.552
> undo
> ui mousemode right select
> ui mousemode right translate
> ui mousemode right "move picked models"
> undo
[Repeated 8 time(s)]
> select clear
> select #7/J
83 atoms, 93 bonds, 4 residues, 1 model selected
> ui mousemode right select
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.64006,0.12593,-0.75793,123.61,-0.73433,0.39043,-0.55527,253.06,0.22599,0.91198,0.34238,-55.043
> undo
> close #7
> help swapna
No help found for 'swapna'
> close #2
> close #5
> open "/Users/luca/Dropbox (Cambridge University)/RAD51/Papers/Abasic DNA
> filament/CryoEM/Figure 2 - cryoem/APdsDNA_noAP.pdb"
Chain information for APdsDNA_noAP.pdb #2
---
Chain | Description
A B C D E F I | No description available
L | No description available
M | No description available
> show cartoons
> hide atoms
> select nucleic-acid
1809 atoms, 2021 bonds, 92 residues, 2 models selected
> hide sel cartoons
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 1809 atom styles
> view matrix models
> #6,1,0,0,0.83746,0,1,0,0.23462,0,0,1,-5.0302,#2,1,0,0,0.83746,0,1,0,0.23462,0,0,1,-5.0302
> view matrix models
> #6,1,0,0,0.92955,0,1,0,0.30492,0,0,1,-6.1255,#2,1,0,0,0.92955,0,1,0,0.30492,0,0,1,-6.1255
> select clear
> hide #!2 models
> show #!2 models
> hide #!6 models
> show #!8 models
> show #!3 models
> hide #!3 models
> hide #!8 models
> show #!3 models
> hide #!2 models
> show #!6 models
> close #1-4,6,8
> open "/Users/luca/Dropbox (Cambridge University)/RAD51/Structures/RAD51-AP-
> dsDNA/phenix/RealSpaceRefine_2/APdsDNA_02.03_real_space_refined_002.pdb"
Chain information for APdsDNA_02.03_real_space_refined_002.pdb #1
---
Chain | Description
A B C D E F I | No description available
L | No description available
M | No description available
> hide atoms
> show cartoons
> open "/Users/luca/Dropbox (Cambridge University)/RAD51/Papers/Abasic DNA
> filament/CryoEM/Figure 2 - cryoem/APdsDNA_noAP.pdb"
Chain information for APdsDNA_noAP.pdb #2
---
Chain | Description
A B C D E F I | No description available
L | No description available
M | No description available
> hide atoms
> show cartoons
> select nucleic-acid
1809 atoms, 2021 bonds, 92 residues, 2 models selected
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 1809 atom styles
> hide sel cartoons
> select clear
> open "/Users/luca/Dropbox (Cambridge University)/RAD51/Structures/RAD51-AP-
> dsDNA/Abasic-filament-
> old/Phenix/LocalAnisoSharpen_2/run_half1_class001_unfil_and_run_half2_class001_unfil_sharpened.ccp4"
Opened run_half1_class001_unfil_and_run_half2_class001_unfil_sharpened.ccp4 as
#3, grid size 200,200,200, pixel 1.3, shown at level 0.0144, step 1, values
float32
> help volume
> volume #1 surfaceSmoothing true subdivideSurface true
No volumes specified
> volume #3 surfaceSmoothing true subdivideSurface true
> volume zone #3 nearAtoms #1/M,L range 2 newMap true
Opened run_half1_class001_unfil_and_run_half2_class001_unfil_sharpened.ccp4
zone as #4, grid size 200,200,200, pixel 1.3, shown at step 1, values float32
> volume zone #3 nearAtoms #2/M,L range 2 newMap true
Opened run_half1_class001_unfil_and_run_half2_class001_unfil_sharpened.ccp4
zone as #5, grid size 200,200,200, pixel 1.3, shown at step 1, values float32
> hide #!1 models
> hide #!2 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> volume #5 level 0.01422
> volume #5 level 0.01688
> select add #4
2 models selected
> transparency sel 50
> select clear
> volume #5 level 0.01483
> open "/Users/luca/Dropbox (Cambridge University)/RAD51/Structures/RAD51-AP-
> dsDNA/Abasic-filament-old/maps/6asm_AR.mrc"
Opened 6asm_AR.mrc as #6, grid size 200,200,200, pixel 1.3, shown at level
0.012, step 1, values float32
> volume #6 surfaceSmoothing true subdivideSurface true
> volume zone #6 nearAtoms #1/M,L range 2 newMap true
Opened 6asm_AR.mrc zone as #7, grid size 200,200,200, pixel 1.3, shown at step
1, values float32
> volume zone #6 nearAtoms #2/M,L range 2 newMap true
Opened 6asm_AR.mrc zone as #8, grid size 200,200,200, pixel 1.3, shown at step
1, values float32
> hide #!5 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> hide #!7 models
> show #!7 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> volume #8 level 0.01199
> volume #8 level 0.01209
> volume #8 level 0.01282
> hide #!7 models
> show #!7 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> transparency #7.1#8.1 50
> select nucleic-acid
1809 atoms, 2021 bonds, 92 residues, 2 models selected
> show #!1 models
> select clear
> select protein
33376 atoms, 33852 bonds, 14 pseudobonds, 4354 residues, 4 models selected
> hide sel & #!1 cartoons
> select clear
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> volume #8 level 0.0122
> show #!7 models
> hide #!8 models
> volume #7 surfaceSmoothing true subdivideSurface true
> show #!8 models
> hide #!7 models
> volume #8 surfaceSmoothing true subdivideSurface true
> select clear
> show #!7 models
> hide #!7 models
> select add #8
2 models selected
> ui tool show "Color Actions"
> color sel dark gray target s
> color sel dim gray target s
> color sel dark gray target s
> color sel gray target s
> color sel dark gray target s
> select clear
> select #1/L
453 atoms, 506 bonds, 23 residues, 1 model selected
> select clear
> select #1/M:21@OP1
1 atom, 1 residue, 1 model selected
> select clear
> select #1/M
413 atoms, 459 bonds, 23 residues, 1 model selected
> ui tool show "Color Actions"
> color sel orange target a
> select clear
> hide #!8 models
> show #!8 models
> show #!7 models
> hide #!7 models
> close #4-5
> close #3
> ui tool show "Side View"
> graphics silhouettes false
> nucleotides #!1 fill
> style nucleic & #!1 stick
Changed 866 atom styles
> nucleotides #!1 atoms
> style nucleic & #!1 stick
Changed 866 atom styles
> nucleotides #!1 fill
> style nucleic & #!1 stick
Changed 866 atom styles
> nucleotides #!1 atoms
> style nucleic & #!1 stick
Changed 866 atom styles
> graphics silhouettes true
> hide #!8 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 1 model selected
> select clear
> select ::name="3DR"
77 atoms, 77 bonds, 7 residues, 1 model selected
> color sel orange red target a
> color sel red target a
> select clear
> select #1/M
413 atoms, 459 bonds, 23 residues, 1 model selected
> color sel khaki target a
> color sel wheat target a
> color sel khaki target a
> color sel wheat target a
> select clear
> select ::name="3DR"
77 atoms, 77 bonds, 7 residues, 1 model selected
> color sel orange target a
> select clear
> select #1/L
453 atoms, 506 bonds, 23 residues, 1 model selected
> color sel rosy brown target a
> color sel tan target a
> color sel rosy brown target a
> color sel brown target a
> color sel chocolate target a
> color sel sienna target a
> color sel indian red target a
> color sel dark goldenrod target a
> color sel peru target a
> color sel saddle brown target a
> color sel brown target a
> color sel rosy brown target a
[Repeated 1 time(s)]
> select clear
> show #!8 models
> select ::name="3DR"
77 atoms, 77 bonds, 7 residues, 1 model selected
> color sel yellow target a
> select clear
> select ::name="3DR"
77 atoms, 77 bonds, 7 residues, 1 model selected
> color sel cyan target a
> color sel orange target a
> select clear
> select add #8
2 models selected
> color sel light steel blue target s
> select clear
> select #1/M
413 atoms, 459 bonds, 23 residues, 1 model selected
> color sel rosy brown target a
> select ::name="3DR"
77 atoms, 77 bonds, 7 residues, 1 model selected
> color sel orange target a
> select clear
> ui tool show "Side View"
> save "/Users/luca/Dropbox (Cambridge University)/RAD51/Papers/Abasic DNA
> filament/CryoEM/Figure 2 - cryoem/RAD51-AP-dsDNA.cxs"
> save "/Users/luca/Dropbox (Cambridge University)/RAD51/Papers/Abasic DNA
> filament/CryoEM/Figure 2 - cryoem/map_DNAonly.png" width 2857 height 2400
> supersample 3
> hide #!8 models
> select add #1
17785 atoms, 18122 bonds, 7 pseudobonds, 2244 residues, 2 models selected
> select clear
> select nucleic-acid
1809 atoms, 2021 bonds, 92 residues, 2 models selected
> show sel & #!1 atoms
> style sel & #!1 sphere
Changed 866 atom styles
> select clear
> select protein
33376 atoms, 33852 bonds, 14 pseudobonds, 4354 residues, 4 models selected
> show sel & #!1 cartoons
> color sel light steel blue target c
[Repeated 1 time(s)]
> select clear
> graphics silhouettes false
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting full
> lighting shadows false
> dssp #1
> select adenine|cytosine|guanine|thymine|uracil
937 atoms, 990 bonds, 99 residues, 2 models selected
> color sel tan target a
> color sel khaki target a
> color sel wheat target a
> select clear
> graphics silhouettes false
> lighting soft
> lighting flat
> lighting full
> lighting shadows false
> graphics silhouettes false
> lighting simple
> lighting shadows true
> lighting simple
> lighting soft
> lighting shadows true intensity 0.5
> lighting full
[Repeated 1 time(s)]
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting soft
> select add #1
17785 atoms, 18122 bonds, 7 pseudobonds, 2244 residues, 2 models selected
> view #1 clip false
> select clear
> select ::name="3DR"
77 atoms, 77 bonds, 7 residues, 1 model selected
> color sel yellow target a
> select clear
> save "/Users/luca/Dropbox (Cambridge University)/RAD51/Papers/Abasic DNA
> filament/CryoEM/Figure 2 - cryoem/RAD51-AP-dsDNA.png" width 2857 height 2400
> supersample 3
> select adenine|cytosine|guanine|thymine|uracil
937 atoms, 990 bonds, 99 residues, 2 models selected
> color sel wheat target a
> color sel beige target a
> color sel burly wood target a
> color sel beige target a
> color sel wheat target a
> color sel peach puff target a
> color sel rosy brown target a
> color sel tan target a
> color sel burly wood target a
> color sel tan target a
> color sel dark khaki target a
> color sel tan target a
> select clear
> save "/Users/luca/Dropbox (Cambridge University)/RAD51/Papers/Abasic DNA
> filament/CryoEM/Figure 2 - cryoem/RAD51-AP-dsDNA.png" width 2857 height 2400
> supersample 3
> select ::name="3DR"
77 atoms, 77 bonds, 7 residues, 1 model selected
> ui tool show "Color Actions"
> color sel pale green target a
> color sel light green target a
> color sel light cyan target a
> color sel aquamarine target a
> color sel magenta target a
> color sel deep pink target a
> color sel orchid target a
> color sel plum target a
> color sel violet target a
> color sel lavender target a
> color sel plum target a
> color sel violet target a
> color sel magenta target a
> color sel deep pink target a
> color sel dark violet target a
> color sel hot pink target a
> color sel orchid target a
> color sel magenta target a
> color sel hot pink target a
> color sel magenta target a
> color sel medium violet red target a
> color sel pale violet red target a
> color sel medium purple target a
> color sel pale violet red target a
> color sel medium purple target a
> color sel purple target a
> color sel dark magenta target a
> color sel dark orchid target a
[Repeated 1 time(s)]
> color sel medium violet red target a
> color sel medium orchid target a
[Repeated 1 time(s)]
> color sel orchid target a
> color sel hot pink target a
[Repeated 1 time(s)]
> color sel deep pink target a
> color sel hot pink target a
> color sel deep pink target a
> select clear
> save "/Users/luca/Dropbox (Cambridge University)/RAD51/Papers/Abasic DNA
> filament/CryoEM/Figure 2 - cryoem/RAD51-AP-dsDNA.png" width 2857 height 2400
> supersample 3
> select protein
33376 atoms, 33852 bonds, 14 pseudobonds, 4354 residues, 4 models selected
> hide sel & #!1 cartoons
> select nucleic-acid
1809 atoms, 2021 bonds, 92 residues, 2 models selected
> nucleotides sel & #!1 atoms
> style nucleic & sel & #!1 stick
Changed 866 atom styles
> show #!8 models
> select clear
[Repeated 1 time(s)]
> graphics silhouettes true
> lighting simple
> lighting soft
> lighting full
> lighting simple
> lighting full
[Repeated 1 time(s)]
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting simple
> graphics silhouettes false
> lighting shadows true
> lighting shadows false
> lighting full
> graphics silhouettes true
> lighting simple
> lighting full
[Repeated 1 time(s)]
> lighting simple
> lighting full
> lighting simple
> save "/Users/luca/Dropbox (Cambridge University)/RAD51/Papers/Abasic DNA
> filament/CryoEM/Figure 2 - cryoem/map_DNAonly.png" width 2857 height 2400
> supersample 3
> rename #8 6asm_AR.mrc zone around DNA (filled APs)
Expected a keyword
> rename #8 "6asm_AR.mrc zone around DNA (filled APs)"
> rename #7 "6asm_AR.mrc zone around DNA"
> rename #2 "APdsDNA_02.03_real_space_refined_002.pdb (filled APs)"
> rename #6 "6asm_AR.mrc (3D refine map)"
> save "/Users/luca/Dropbox (Cambridge University)/RAD51/Papers/Abasic DNA
> filament/CryoEM/Figure 2 - cryoem/RAD51-AP-dsDNA.cxs"
——— End of log from Fri Mar 3 13:15:08 2023 ———
opened ChimeraX session
> hide #!8 models
> show #!1 cartoons
> view view1
> select nucleic-acid
1809 atoms, 2021 bonds, 92 residues, 2 models selected
> show sel & #!1 atoms
> hide sel & #!1 cartoons
> style sel & #!1 sphere
Changed 866 atom styles
> select clear
> graphics silhouettes false
> lighting simple
> lighting soft
> select ::name="ATP"
434 atoms, 462 bonds, 14 residues, 2 models selected
> show sel & #!1 atoms
> ui tool show "Color Actions"
> color sel dodger blue target a
> select clear
> save "/Users/luca/Dropbox (Cambridge University)/RAD51/Papers/Abasic DNA
> filament/CryoEM/Figure 2 - cryoem/RAD51-AP-dsDNA.cxs"
> save "/Users/luca/Dropbox (Cambridge University)/RAD51/Papers/Abasic DNA
> filament/CryoEM/Figure 2 - cryoem/RAD51-AP-dsDNA.png" width 2857 height 2400
> supersample 3
> save "/Users/luca/Dropbox (Cambridge University)/RAD51/Papers/Abasic DNA
> filament/CryoEM/Figure 2 - cryoem/RAD51-AP-dsDNA.cxs"
——— End of log from Fri Mar 3 18:07:51 2023 ———
opened ChimeraX session
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!6 models
> hide #!1 models
> show #!7 models
> hide #!6 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> transparency #7.1 0
> show #!1 models
> hide #!7 models
> select ::name="DA"::name="DC"::name="DG"::name="DT"
1732 atoms, 1930 bonds, 85 residues, 2 models selected
> select clear
> select #1/L:18@N4
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 20 bonds, 1 residue, 1 model selected
> select up
453 atoms, 506 bonds, 23 residues, 1 model selected
> select add #1/M:15@C3'
454 atoms, 506 bonds, 24 residues, 1 model selected
> select up
464 atoms, 517 bonds, 24 residues, 1 model selected
> select up
866 atoms, 965 bonds, 46 residues, 1 model selected
> select down
464 atoms, 517 bonds, 24 residues, 1 model selected
> select add #1/M:16@C5'
465 atoms, 517 bonds, 25 residues, 1 model selected
> select up
484 atoms, 539 bonds, 25 residues, 1 model selected
> select up
866 atoms, 965 bonds, 46 residues, 1 model selected
> nucleotides sel atoms
> style nucleic & sel stick
Changed 866 atom styles
> select clear
> open "/Users/luca/Dropbox (Cambridge University)/RAD51/Structures/RAD51-AP-
> dsDNA/PDB:EMDB deposition/ap5_dsDNA_05_real_space_refined_047.pdb"
Chain information for ap5_dsDNA_05_real_space_refined_047.pdb #3
---
Chain | Description
A B C D E F G H | No description available
I | No description available
J | No description available
> show #!1,3 cartoons
> hide #!1,3 atoms
> hide #!1 models
> open "/Users/luca/Dropbox (Cambridge University)/RAD51/Structures/PDB
> deposition - second metal ion structures/post-NPF/coords/post-npf.pdb"
Chain information for post-npf.pdb #4
---
Chain | Description
A B C D E F | No description available
G | No description available
H | No description available
> show #!3-4 cartoons
> hide #!3-4 atoms
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> select add #4
15442 atoms, 15624 bonds, 2044 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,-65.228,0,1,0,-69.061,0,0,1,-12.412
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.15034,0.82644,-0.54257,43.245,-0.75042,0.2619,0.60686,59.396,0.64363,0.49839,0.58081,-116.51
> view matrix models
> #4,-0.66068,0.62579,-0.4146,124.55,-0.41638,0.15405,0.89604,-8.1117,0.6246,0.76463,0.15879,-97.118
> view matrix models
> #4,-0.77636,0.23126,0.58634,66.508,0.43446,-0.4776,0.76363,-16.034,0.45663,0.84759,0.27032,-100.69
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.77636,0.23126,0.58634,43.989,0.43446,-0.4776,0.76363,-44.173,0.45663,0.84759,0.27032,-101.2
> view matrix models
> #4,-0.77636,0.23126,0.58634,45.112,0.43446,-0.4776,0.76363,-43.328,0.45663,0.84759,0.27032,-103.59
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.66151,0.51578,0.54441,-5.7019,0.1019,-0.65739,0.74663,29.715,0.74298,0.54938,0.38231,-114.37
> select clear
> ui tool show Matchmaker
> matchmaker #4/C to #3/D pairing ss
Parameters
---
Chain pairing | ss
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 ap5_dsDNA_05_real_space_refined_047.pdb, chain D (#3) with post-
npf.pdb, chain C (#4), sequence alignment score = 1569.6
RMSD between 311 pruned atom pairs is 0.343 angstroms; (across all 311 pairs:
0.343)
> hide #!4 models
> show #!4 models
> select #4/G:12
19 atoms, 20 bonds, 1 residue, 1 model selected
> select up
414 atoms, 464 bonds, 20 residues, 1 model selected
> select add #3/I:10
434 atoms, 485 bonds, 21 residues, 2 models selected
> select up
827 atoms, 923 bonds, 43 residues, 2 models selected
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 827 atom styles
> select #4/H:10
21 atoms, 23 bonds, 1 residue, 1 model selected
> select up
406 atoms, 454 bonds, 20 residues, 1 model selected
> select add #3/J:11
427 atoms, 477 bonds, 21 residues, 2 models selected
> select up
859 atoms, 960 bonds, 43 residues, 2 models selected
> hide sel cartoons
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 859 atom styles
> select clear
> select #3/D:274
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
31 atoms, 30 bonds, 4 residues, 1 model selected
> select add #4/C:274
39 atoms, 37 bonds, 5 residues, 2 models selected
> select up
62 atoms, 60 bonds, 8 residues, 2 models selected
> show sel atoms
> style sel stick
Changed 62 atom styles
> select #4/B:235
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #3/C:235
22 atoms, 20 bonds, 2 residues, 2 models selected
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> style sel stick
Changed 22 atom styles
> select #4/C:271
5 atoms, 4 bonds, 1 residue, 1 model selected
> select subtract #4/C:271
Nothing selected
> select add #4/C:271
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #3/D:271
10 atoms, 8 bonds, 2 residues, 2 models selected
> show sel atoms
> style sel stick
Changed 10 atom styles
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> save "/Users/luca/Dropbox (Cambridge University)/RAD51/Papers/Abasic DNA
> filament/CryoEM/Figure 2 - cryoem/RAD51-AP-dsDNA.cxs" includeMaps true
——— End of log from Fri Feb 23 16:06:03 2024 ———
opened ChimeraX session
> select clear
> close #4
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> open "/Users/lp212/Dropbox (Cambridge University)/RAD51/Structures/PDB
> deposition - second metal ion structures/post-NPF/coords/post-npf.pdb"
Chain information for post-npf.pdb #4
---
Chain | Description
A B C D E F | No description available
G | No description available
H | No description available
> show #!3-4 cartoons
> hide #!3-4 atoms
> open "/Users/lp212/Dropbox (Cambridge University)/RAD51/Structures/PDB
> deposition - second metal ion structures/post-NPF/maps/RAD51 Postsynaptic
> 2.9A.mrc"
Opened RAD51 Postsynaptic 2.9A.mrc as #5, grid size 204,204,204, pixel 1.3,
shown at level 0.0266, step 1, values float32
> ui tool show Matchmaker
[Repeated 1 time(s)]Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/tool.py", line 279, in run_matchmaker
cmd += ' bring ' + concise_model_spec(self.session, models)
^^^^^^^^^^^^^^^^^^
UnboundLocalError: cannot access local variable 'concise_model_spec' where it
is not associated with a value
UnboundLocalError: cannot access local variable 'concise_model_spec' where it
is not associated with a value
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/tool.py", line 279, in run_matchmaker
cmd += ' bring ' + concise_model_spec(self.session, models)
^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Model Number: MKGT3B/A
Chip: Apple M1 Pro
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 8422.141.2
OS Loader Version: 8422.141.2
Software:
System Software Overview:
System Version: macOS 13.5 (22G74)
Kernel Version: Darwin 22.6.0
Time since boot: 2 days, 18 hours, 32 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
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:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
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: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
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: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
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: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
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: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
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: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
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: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
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: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 20 months ago
| Component: | Unassigned → Structure Comparison |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → MatchMaker: cannot access local variable 'concise_model_spec' |
comment:2 by , 20 months ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
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Hi Luca,
--Eric