Opened 21 months ago

Closed 21 months ago

#14636 closed defect (fixed)

MatchMaker: cannot access local variable 'concise_model_spec'

Reported by: lp212@… Owned by: Eric Pettersen
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 Eric Pettersen, 21 months ago

Component: Unassigned → Structure Comparison
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → MatchMaker: cannot access local variable 'concise_model_spec'

comment:2 by Eric Pettersen, 21 months ago

Resolution: → fixed
Status: accepted → closed

Hi Luca,

Thanks for reporting this problem. It only occurs when doing specific-chain-to-specific-chain matching and you are "bringing" other models along with the match. I have fixed the bug and the fix will be in the next daily build.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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