![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 8 hours ago
Last modified 6 hours ago
#20051 assigned defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | chimera-programmers | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-26.3.1-arm64-arm-64bit
ChimeraX Version: 1.12.dev202602270247 (2026-02-27 02:47:46 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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"procLaunch" : "2026-03-23 16:29:05.7881 +0100",
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UNUSED SPACE AT START
--->
__TEXT 102134000-102138000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
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REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
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"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/_mmcif.cpython-311-darwin.so",
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"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/pdb\/_pdbio.cpython-311-darwin.so",
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"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/etree.cpython-311-darwin.so",
"name" : "etree.cpython-311-darwin.so"
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"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/_elementpath.cpython-311-darwin.so",
"name" : "_elementpath.cpython-311-darwin.so"
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"uuid" : "0596a7b6-bce2-3f06-a2e8-3eaab5371ed8",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
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"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
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"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
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Writable regions: Total=1.1G written=1346K(0%) resident=1346K(0%) swapped_out=0K(0%) unallocated=1.1G(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
.note.gnu.proper 320 1
Accelerate framework 256K 2
Activity Tracing 256K 1
AttributeGraph Data 1024K 1
CG image 5104K 5
CG raster data 3296K 7
ColorSync 96K 6
CoreAnimation 1456K 90
CoreGraphics 64K 4
CoreServices 240K 1
CoreUI image data 1408K 16
Foundation 48K 2
Kernel Alloc Once 112K 3
MALLOC 436.5M 121
MALLOC guard page 3504K 4
OpenGL GLSL 256K 3
PROTECTED_MEMORY 16K 1
STACK GUARD 704K 44
Stack 203.5M 45
Stack Guard 56.0M 1
VM_ALLOCATE 250.8M 211
VM_ALLOCATE (reserved) 192.0M 1 reserved VM address space (unallocated)
__AUTH 5843K 644
__AUTH_CONST 89.0M 1026
__CTF 824 1
__DATA 42.9M 1131
__DATA_CONST 60.5M 1172
__DATA_DIRTY 8393K 884
__FONT_DATA 2352 1
__GLSLBUILTINS 5176K 1
__INFO_FILTER 8 1
__LINKEDIT 623.1M 142
__OBJC_RO 78.4M 1
__OBJC_RW 2571K 1
__TEXT 1.5G 1193
__TEXT (graphics) 96K 2
__TPRO_CONST 128K 2
dyld private memory 2304K 19
mapped file 648.5M 73
page table in kernel 1346K 1
shared memory 976K 21
=========== ======= =======
TOTAL 4.2G 6886
TOTAL, minus reserved VM space 4.0G 6886
",
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Log:
UCSF ChimeraX version: 1.12.dev202602270247 (2026-02-27)
© 2016-2026 Regents of the University of California. All rights reserved.
> open "/Users/anz/Desktop/P-motifs 260223 GLS.cxs"
Log from Tue Feb 24 10:12:16 2026UCSF ChimeraX version: 1.11.dev202511180234
(2025-11-18)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/anz/Desktop/P-motifs 260222.cxs" format session
Log from Sat Feb 21 18:41:51 2026UCSF ChimeraX version: 1.11.dev202511180234
(2025-11-18)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/anz/Desktop/P-motifs/2025 RAD54B paper/2025 experiments/XX25-36
> GST pull-down DMC1 mutants negatively charged/260127 54B positive and DMC1
> negative residues tested in XX25-36.cxs"
Log from Wed Jan 28 15:35:48 2026UCSF ChimeraX version: 1.11.dev202511180234
(2025-11-18)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/anz/Desktop/P-motifs/2025 RAD54B paper/2025
> experiments/251020_lysines.cxs"
Log from Tue Oct 21 09:05:15 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/anz/Desktop/P-motifs/2025 RAD54B paper/2025
> experiments/251009_lysines.cxs"
Opened cryosparc_P26_J410_011_volume_map_sharp.mrc as #2.1, grid size
336,336,336, pixel 0.73, shown at level 0.032, step 2, values float32
Opened cryosparc_P26_J410_011_volume_map.mrc as #2.2, grid size 336,336,336,
pixel 0.73, shown at level 0.0225, step 2, values float32
Log from Mon Oct 13 17:24:42 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/anz/Desktop/251009_lysines.cxs
Opened cryosparc_P26_J410_011_volume_map_sharp.mrc as #2.1, grid size
336,336,336, pixel 0.73, shown at level 0.032, step 2, values float32
Opened cryosparc_P26_J410_011_volume_map.mrc as #2.2, grid size 336,336,336,
pixel 0.73, shown at level 0.0225, step 2, values float32
Log from Thu Oct 9 18:29:50 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/anz/Desktop/251009_lysines.cxs
Opened cryosparc_P26_J410_011_volume_map_sharp.mrc as #2.1, grid size
336,336,336, pixel 0.73, shown at level 0.032, step 2, values float32
Opened cryosparc_P26_J410_011_volume_map.mrc as #2.2, grid size 336,336,336,
pixel 0.73, shown at level 0.0225, step 2, values float32
Log from Thu Oct 9 14:13:54 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/anz/Desktop/P-motifs/2025 RAD54B paper/250904 TMM
> RAD54B/preparation/ForAlexRAD54B movies TMM peptide 2.cxs"
Opened cryosparc_P26_J410_011_volume_map_sharp.mrc as #2.1, grid size
336,336,336, pixel 0.73, shown at level 0.032, step 2, values float32
Opened cryosparc_P26_J410_011_volume_map.mrc as #2.2, grid size 336,336,336,
pixel 0.73, shown at level 0.0225, step 2, values float32
Log from Thu Sep 4 04:53:36 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/anz/Desktop/P-motifs/2025 RAD54B paper/data/250712 CryoEM
> structures RAD54B PhePP from Sophie/ForAlexRAD54B movies TMM.cxs"
Opened cryosparc_P26_J410_011_volume_map_sharp.mrc as #2.1, grid size
336,336,336, pixel 0.73, shown at level 0.032, step 2, values float32
Opened cryosparc_P26_J410_011_volume_map.mrc as #2.2, grid size 336,336,336,
pixel 0.73, shown at level 0.0225, step 2, values float32
Log from Wed Sep 3 19:35:27 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/anz/Desktop/P-motifs/2025 RAD54B paper/data/250712 CryoEM
> structures RAD54B PhePP from Sophie/ForAlexRAD54B.cxs"
Opened cryosparc_P26_J410_011_volume_map_sharp.mrc as #2.1, grid size
336,336,336, pixel 0.73, shown at level 0.032, step 2, values float32
Opened cryosparc_P26_J410_011_volume_map.mrc as #2.2, grid size 336,336,336,
pixel 0.73, shown at level 0.0225, step 2, values float32
Log from Fri Jul 11 19:20:58 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
> RAD54/RAD54B.cxs" format session
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Opened cryosparc_P26_J362_012_volume_map_sharp.mrc as #6, grid size
336,336,336, pixel 0.73, shown at level 0.05, step 2, values float32
Opened cryosparc_P26_J362_012_volume_map.mrc as #8, grid size 336,336,336,
pixel 0.73, shown at level 0.0236, step 2, values float32
Opened cryosparc_P26_J410_011_volume_map_sharp.mrc as #9, grid size
336,336,336, pixel 0.73, shown at level 0.0229, step 2, values float32
restore_snapshot for "Redust" returned None
Log from Thu Jul 10 10:47:21 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
> RAD54/BRCA2-07072025.cxs"
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Opened cryosparc_P26_J362_012_volume_map_sharp.mrc as #6, grid size
336,336,336, pixel 0.73, shown at level 0.035, step 2, values float32
Opened cryosparc_P26_J402_011_volume_map.mrc as #1, grid size 336,336,336,
pixel 0.745, shown at level 0.0227, step 2, values float32
Opened cryosparc_P26_J402_011_volume_map_sharp.mrc as #2, grid size
336,336,336, pixel 0.745, shown at level 0.0194, step 2, values float32
Log from Mon Jul 7 15:58:39 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/sz140275local/Downloads/J216_011_volume_map_ABCEF.pdb
Chain information for J216_011_volume_map_ABCEF.pdb #1
---
Chain | Description
A B C D E F | No description available
M N O P Q R | No description available
X | No description available
> open
> /Users/sz140275local/Downloads/cryosparc_P26_J216_011_volume_map_sharp.mrc
Opened cryosparc_P26_J216_011_volume_map_sharp.mrc as #2, grid size
336,336,336, pixel 0.745, shown at level 0.0337, step 2, values float32
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> volume #2 level 0.1509
> hide #!2 models
> hide atoms
> show cartoons
Computing secondary structure
> select #1/B
2438 atoms, 2476 bonds, 1 pseudobond, 314 residues, 2 models selected
> color sel light green
> select #1/C
2438 atoms, 2476 bonds, 1 pseudobond, 314 residues, 2 models selected
> color sel light blue
> select #1/D
2438 atoms, 2476 bonds, 1 pseudobond, 314 residues, 2 models selected
> color sel light green
> select #1/F
2438 atoms, 2476 bonds, 1 pseudobond, 314 residues, 2 models selected
> color sel light green
> select add #1
15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 2 models selected
> select subtract #1
Nothing selected
> show #!2 models
> volume #2 level 0.08302
> transparency 50
> volume #2 level 0.03522
> surface dust #2 size 7.45
> color zone #2 near #1 distance 4.47
> transparency 0
> transparency 50
> ui mousemode right zoom
> select #1/O
55 atoms, 58 bonds, 7 residues, 1 model selected
> show sel atoms
> select add #1
15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 2 models selected
> select subtract #1
Nothing selected
> ui mousemode right translate
> select #1/P
55 atoms, 58 bonds, 7 residues, 1 model selected
> show sel atoms
> select add #1
15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 2 models selected
> select subtract #1
Nothing selected
> volume #2 level 0.02134
> surface dust #2 size 7.45
> color zone #2 near #1 distance 4.47
> transparency 0
> transparency 50
> volume #2 level 0.02443
> color zone #2 near #1 distance 4.47
> transparency 0
> transparency 50
> open /Users/sz140275local/Downloads/cryosparc_P26_J216_011_volume_map.mrc
Opened cryosparc_P26_J216_011_volume_map.mrc as #3, grid size 336,336,336,
pixel 0.745, shown at level 0.0204, step 2, values float32
> hide #!2 models
> ui tool show "Fit in Map"
> fitmap #1 inMap #3
Fit molecule J216_011_volume_map_ABCEF.pdb (#1) to map
cryosparc_P26_J216_011_volume_map.mrc (#3) using 15318 atoms
average map value = 0.04976, steps = 44
shifted from previous position = 0.00864
rotated from previous position = 0.0468 degrees
atoms outside contour = 2325, contour level = 0.020397
Position of J216_011_volume_map_ABCEF.pdb (#1) relative to
cryosparc_P26_J216_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999981 0.00023261 0.00057087 -0.10686852
-0.00023292 0.99999983 0.00053698 -0.03534062
-0.00057074 -0.00053712 0.99999969 0.14093574
Axis -0.65688580 0.69817168 -0.28470573
Axis point 249.53117123 0.00000000 181.07164593
Rotation angle (degrees) 0.04684334
Shift along axis 0.00540138
> fitmap #1 inMap #3
Fit molecule J216_011_volume_map_ABCEF.pdb (#1) to map
cryosparc_P26_J216_011_volume_map.mrc (#3) using 15318 atoms
average map value = 0.04976, steps = 40
shifted from previous position = 0.0138
rotated from previous position = 0.00839 degrees
atoms outside contour = 2325, contour level = 0.020397
Position of J216_011_volume_map_ABCEF.pdb (#1) relative to
cryosparc_P26_J216_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999978 0.00031309 0.00057735 -0.11718292
-0.00031333 0.99999986 0.00041488 -0.02267100
-0.00057722 -0.00041506 0.99999975 0.12663259
Axis -0.53414014 0.74307156 -0.40316122
Axis point 215.58542420 0.00000000 207.95751060
Rotation angle (degrees) 0.04451256
Shift along axis -0.00530742
> transparency #3.1 50
> volume #3 level 0.01092
> surface dust #3 size 7.45
> color zone #3 near #1 distance 4.47
> transparency #3.1 0
> transparency #3.1 50
> hide #!3 models
> select #1/P
55 atoms, 58 bonds, 7 residues, 1 model selected
> color sel red
> hide #!1 models
> show #!1 models
> select add #1
15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 2 models selected
> select subtract #1
Nothing selected
> show #!3 models
> color zone #3 near #1 distance 4.47
> transparency #3.1 0
> transparency #3.1 50
> label sel
> label #1/P
> hide #!3 models
> show #!3 models
> hide #!3 models
> select #1/D
2438 atoms, 2476 bonds, 1 pseudobond, 314 residues, 2 models selected
> show sel atoms
[Repeated 1 time(s)]
> style sel stick
Changed 2438 atom styles
> show #!3 models
> select add #1
15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 3 models selected
> select subtract #1
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> volume #3 level 0.01255
> color zone #3 near #1 distance 4.47
> transparency #3.1 0
> transparency #3.1 50
> volume #3 level 0.01549
> color zone #3 near #1 distance 4.47
> select #1/O
55 atoms, 58 bonds, 7 residues, 1 model selected
> color sel red
> color zone #3 near sel & #1 distance 4.47
[Repeated 2 time(s)]
> select #1/P
55 atoms, 58 bonds, 7 residues, 1 model selected
> select #1/P
55 atoms, 58 bonds, 7 residues, 1 model selected
> color sel red
> color zone #3 near sel & #1 distance 4.47
> select add #1
15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 3 models selected
> select subtract #1
Nothing selected
> select add #1
15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 3 models selected
> color zone #3 near sel & #1 distance 4.47
> select #1/Q
55 atoms, 58 bonds, 7 residues, 1 model selected
> select #1/Q,N
110 atoms, 116 bonds, 14 residues, 1 model selected
> color sel red
> color zone #3 near sel & #1 distance 4.47
[Repeated 1 time(s)]
> select add #1
15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 3 models selected
> select subtract #1
Nothing selected
> select add #1
15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 3 models selected
> color zone #3 near sel & #1 distance 4.47
> select subtract #1
Nothing selected
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> transparency #3.1 0
> transparency #3.1 50
> label #1/O
> label #1/D
> hide atoms
> unlabel #1/D
Unknown command: unlabel #1/D
> unlabel
Unknown command: unlabel
> ~label #1,3 residues
> hide #!3 models
> show #!3 models
> select #1/O
55 atoms, 58 bonds, 7 residues, 1 model selected
> show sel atoms
> label #1/O
> select add #1
15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 3 models selected
> select subtract #1
Nothing selected
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> select #1/C:20
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select #1/C
2438 atoms, 2476 bonds, 1 pseudobond, 314 residues, 2 models selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for J216_011_volume_map_ABCEF.pdb_C SES surface #1.3:
minimum, -26.80, mean -0.75, maximum 13.89
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic sel
Coulombic values for J216_011_volume_map_ABCEF.pdb_C SES surface #1.3:
minimum, -26.80, mean -0.75, maximum 13.89
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!3 models
> select add #1
15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 4 models selected
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> transparency sel 50
> transparency sel 0
> transparency sel 50
> transparency sel 0
> select subtract #1
1 model selected
> select #1/D:89
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> transparency #1.3 50
> select add #1
15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 3 models selected
> select subtract #1
1 model selected
> show #!3 models
> hide #!3 models
> hide surfaces
> show #!3 models
> hide #!3 models
> select #1/M
55 atoms, 58 bonds, 7 residues, 1 model selected
> color sel red
> show #!3 models
> color zone #3 near sel & #1 distance 4.47
[Repeated 1 time(s)]
> select add #1
15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 3 models selected
> select subtract #1
1 model selected
> color zone #3 near #1 distance 4.47
> hide #!1 models
> open emdb:16432
Summary of feedback from opening 16432 fetched from emdb
---
notes | Fetching compressed map 16432 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-16432/map/emd_16432.map.gz
Fetching map header 16432 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-16432/header/emd-16432.xml
Opened emdb 16432 as #4, grid size 600,600,600, pixel 0.73, shown at level
0.0272, step 4, values float32
> hide #!3 models
> open 7bdx
Summary of feedback from opening 7bdx fetched from pdb
---
note | Fetching compressed mmCIF 7bdx from http://files.rcsb.org/download/7bdx.cif
7bdx title:
Armadillo domain of HSF2BP in complex with BRCA2 peptide [more info...]
Chain information for 7bdx #5
---
Chain | Description | UniProt
A B C D | Heat shock factor 2-binding protein | HSF2B_HUMAN 122-334
E F | Breast cancer type 2 susceptibility protein | BRCA2_HUMAN 2291-2343
Non-standard residues in 7bdx #5
---
MG — magnesium ion
> hide #!4 models
> view #5 clip false
> hide #!5 atoms
> show #!5 cartoons
> select #5/E,F
871 atoms, 854 bonds, 135 residues, 1 model selected
> color sel red
> select add #5
7434 atoms, 7385 bonds, 2 pseudobonds, 1110 residues, 2 models selected
> select subtract #5
Nothing selected
> color #5/A
> color #5/A light blue
> color #5/B lime
> color #5/B pale green
> color #5/C pale green
> color #5/C green
> color #5/D cyan
> show #!4 models
> color #4 #fef6d9ff models
> select add #5
7434 atoms, 7385 bonds, 2 pseudobonds, 1110 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #5,1,0,0,105.96,0,1,0,63.522,0,0,1,-12.452
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.13885,0.16272,0.97685,70.836,-0.45432,0.88695,-0.083165,90.344,-0.87995,-0.43226,0.19708,88.131
> view matrix models
> #5,-0.6185,0.067994,0.78284,113.07,-0.18461,0.95579,-0.22887,85.24,-0.76379,-0.28608,-0.5786,118.91
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.6185,0.067994,0.78284,191.52,-0.18461,0.95579,-0.22887,93.923,-0.76379,-0.28608,-0.5786,219.64
> view matrix models
> #5,-0.6185,0.067994,0.78284,99.843,-0.18461,0.95579,-0.22887,143.12,-0.76379,-0.28608,-0.5786,226.59
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.84821,-0.4082,-0.3375,198.72,-0.52089,0.75833,0.39192,131.54,0.095959,0.50824,-0.85585,165.61
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.84821,-0.4082,-0.3375,196.64,-0.52089,0.75833,0.39192,111.25,0.095959,0.50824,-0.85585,238.08
> view matrix models
> #5,-0.84821,-0.4082,-0.3375,207.57,-0.52089,0.75833,0.39192,117.01,0.095959,0.50824,-0.85585,237.86
> ui tool show "Fit in Map"
> fitmap #5 inMap #4
Fit molecule 7bdx (#5) to map emdb 16432 (#4) using 7434 atoms
average map value = 0.03421, steps = 112
shifted from previous position = 7.2
rotated from previous position = 12.8 degrees
atoms outside contour = 2925, contour level = 0.0272
Position of 7bdx (#5) relative to emdb 16432 (#4) coordinates:
Matrix rotation and translation
-0.86382345 -0.47543336 -0.16664985 204.71782263
-0.50378895 0.81675834 0.28125168 124.65891763
0.00239623 0.32690815 -0.94505308 252.37451155
Axis 0.25738757 -0.95299437 -0.15985418
Axis point 113.70622837 0.00000000 121.14343579
Rotation angle (degrees) 174.91163309
Shift along axis -106.45054436
> view matrix models
> #5,-0.86382,-0.47543,-0.16665,208.23,-0.50379,0.81676,0.28125,121.73,0.0023962,0.32691,-0.94505,248.04
> transparency #4.1 50
> view matrix models
> #5,-0.86382,-0.47543,-0.16665,205.91,-0.50379,0.81676,0.28125,124.41,0.0023962,0.32691,-0.94505,248.61
> ui mousemode right translate
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.41993,0.90484,0.070133,95.392,0.15485,-0.0047059,0.98793,111.38,0.89425,0.42572,-0.13814,167.25
> view matrix models
> #5,0.98295,0.008792,-0.18369,115.29,-0.1418,-0.59977,-0.78751,256.29,-0.11709,0.80013,-0.58829,204.52
> view matrix models
> #5,0.44654,0.73647,-0.50815,108.35,-0.66072,-0.11156,-0.7423,242.32,-0.60337,0.66721,0.43678,171.56
> view matrix models
> #5,0.89516,-0.19084,-0.40283,142.43,0.34388,0.87068,0.35167,88.464,0.28362,-0.45333,0.84502,185.29
> view matrix models
> #5,0.65334,-0.40245,-0.64124,176.59,0.62631,0.76315,0.15916,96.048,0.42531,-0.5056,0.75065,188.87
> view matrix models
> #5,0.414,-0.69992,0.58199,133.95,0.24703,0.70175,0.66822,84.089,-0.87611,-0.13288,0.46343,226.97
> view matrix models
> #5,-0.54647,0.35217,0.75984,93.982,0.65193,0.7484,0.12199,98.137,-0.5257,0.56202,-0.63857,235.39
> view matrix models
> #5,-0.2605,0.068669,0.96303,89.77,-0.38401,0.90781,-0.1686,140.11,-0.88582,-0.41373,-0.21011,281.73
> view matrix models
> #5,-0.2192,-0.95749,-0.1875,213.88,-0.32214,-0.11037,0.94024,136.55,-0.92097,0.2665,-0.28425,246.58
> view matrix models
> #5,0.82463,0.2605,-0.50212,123.51,-0.067718,-0.83581,-0.54483,254.24,-0.5616,0.48329,-0.67159,243.15
> view matrix models
> #5,-0.97664,-0.20844,-0.052222,187.44,-0.045686,-0.036052,0.99831,119.48,-0.20997,0.97737,0.025687,162.75
> view matrix models
> #5,-0.73345,-0.15296,-0.66231,210.03,-0.66497,-0.040621,0.74577,154.93,-0.14098,0.9874,-0.071922,165.27
> view matrix models
> #5,-0.74012,0.53192,-0.41145,155.43,-0.3207,-0.81697,-0.47929,258.04,-0.59108,-0.22278,0.77524,205.19
> fitmap #5 inMap #4
Fit molecule 7bdx (#5) to map emdb 16432 (#4) using 7434 atoms
average map value = 0.03392, steps = 280
shifted from previous position = 3.51
rotated from previous position = 37.7 degrees
atoms outside contour = 2888, contour level = 0.0272
Position of 7bdx (#5) relative to emdb 16432 (#4) coordinates:
Matrix rotation and translation
-0.82631357 0.55436000 0.09945286 126.03120258
-0.56321014 -0.81347234 -0.14511058 249.18468833
0.00045865 -0.17591970 0.98440441 173.51218129
Axis -0.02745009 0.08820113 -0.99572439
Axis point 101.14138831 113.49827864 0.00000000
Rotation angle (degrees) 145.86224811
Shift along axis -154.25150712
> view matrix models
> #5,-0.97364,0.19603,0.11663,151.41,-0.22375,-0.7214,-0.65538,260.74,-0.044342,-0.6642,0.74624,217.44
> view matrix models
> #5,-0.58332,-0.28277,0.76143,130.56,-0.44822,-0.66973,-0.59209,261.74,0.67737,-0.68666,0.26392,221.26
> view matrix models
> #5,0.94524,0.30301,0.12123,79.591,0.32533,-0.90438,-0.27615,231.75,0.025962,0.30047,-0.95344,252.77
> fitmap #5 inMap #4
Fit molecule 7bdx (#5) to map emdb 16432 (#4) using 7434 atoms
average map value = 0.02864, steps = 252
shifted from previous position = 21.4
rotated from previous position = 12.1 degrees
atoms outside contour = 3611, contour level = 0.0272
Position of 7bdx (#5) relative to emdb 16432 (#4) coordinates:
Matrix rotation and translation
0.87261982 0.43976226 0.21247070 88.01929926
0.48814924 -0.79925673 -0.35056954 233.42789236
0.01565138 0.40963134 -0.91211688 245.34569372
Axis 0.96624770 0.25016573 0.06150191
Axis point 0.00000000 80.33356484 140.42171784
Rotation angle (degrees) 156.83515700
Shift along axis 158.53333505
> view matrix models
> #5,-0.57905,-0.80598,0.12284,216.52,-0.72635,0.57842,0.37127,152.25,-0.37029,0.12576,-0.92036,275.82
> view matrix models
> #5,-0.74829,-0.61836,0.24019,204.53,-0.049114,0.41273,0.90953,108.97,-0.66155,0.6688,-0.33921,220.85
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.74829,-0.61836,0.24019,197.97,-0.049114,0.41273,0.90953,100.11,-0.66155,0.6688,-0.33921,228.27
> view matrix models
> #5,-0.74829,-0.61836,0.24019,199.07,-0.049114,0.41273,0.90953,97.48,-0.66155,0.6688,-0.33921,224.41
> vop flip #4
Opened emdb 16432 z flip as #6, grid size 600,600,600, pixel 0.73, shown at
step 1, values float32
> view matrix models
> #5,-0.74829,-0.61836,0.24019,182.9,-0.049114,0.41273,0.90953,88.945,-0.66155,0.6688,-0.33921,216
> view matrix models
> #5,-0.74829,-0.61836,0.24019,175.75,-0.049114,0.41273,0.90953,96.632,-0.66155,0.6688,-0.33921,222.71
> volume #6 level 0.06538
> view matrix models
> #5,-0.74829,-0.61836,0.24019,180.22,-0.049114,0.41273,0.90953,87.231,-0.66155,0.6688,-0.33921,240.87
> view matrix models
> #5,-0.74829,-0.61836,0.24019,208.61,-0.049114,0.41273,0.90953,90.379,-0.66155,0.6688,-0.33921,243.87
> volume #6 level 0.03871
> view matrix models
> #5,-0.74829,-0.61836,0.24019,202.27,-0.049114,0.41273,0.90953,112.3,-0.66155,0.6688,-0.33921,212.48
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.88601,-0.4493,0.11449,203.92,0.07525,0.10432,0.99169,121.84,-0.45751,0.88727,-0.058616,176.83
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.88601,-0.4493,0.11449,199.26,0.07525,0.10432,0.99169,116.35,-0.45751,0.88727,-0.058616,182.47
> fitmap #5 inMap #6
Fit molecule 7bdx (#5) to map emdb 16432 z flip (#6) using 7434 atoms
average map value = 0.05131, steps = 436
shifted from previous position = 12.5
rotated from previous position = 67.8 degrees
atoms outside contour = 2238, contour level = 0.038713
Position of 7bdx (#5) relative to emdb 16432 z flip (#6) coordinates:
Matrix rotation and translation
-0.86719186 -0.45679819 -0.19827678 205.88171390
-0.49796702 0.79334082 0.35019880 121.99409785
-0.00266912 0.40242484 -0.91544913 245.49065594
Axis 0.25278458 -0.94678047 -0.19926540
Axis point 113.12491740 0.00000000 116.31534353
Rotation angle (degrees) 174.07068315
Shift along axis -112.37570003
> color zone #6 near sel & #5 distance 4.38
> hide #!5 models
> select subtract #5
Nothing selected
> volume #6 level 0.05326
> color #6 #b1ada080 models
> show #!5 models
> color zone #6 near #5 distance 4.38
> volume #6 level 0.03629
> volume #6 level 0.04114
> hide #!5 models
> transparency #6.1 0
> show #!5 models
> transparency #6.1 50
> hide #!6 models
> open
> /Users/sz140275local/Downloads/ZCWPW1idr_ARMdimer_c8acb/predictions/ZCWPW1idr_ARMdimer/models/ZCWPW1idr_ARMdimer_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_38557.pdb
Chain information for
ZCWPW1idr_ARMdimer_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_38557.pdb
#7
---
Chain | Description
A | No description available
B C | No description available
Computing secondary structure
> hide #!5 models
> view #7 clip false
> color bfactor alphafold palette
> color byattribute bfactor alphafold palette
Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword
> color bfactor #1 alphafold palette
> color byattribute bfactor #1 alphafold palette
Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword
> color bfactor #1 palette alphafold
15318 atoms, 1944 residues, 1 surfaces, atom bfactor range 20 to 100
> color bfactor #1
15318 atoms, 1944 residues, 1 surfaces, atom bfactor range 20 to 100
> color bfactor #7 palette alphafold
4539 atoms, 584 residues, atom bfactor range 16.5 to 98.8
> ui tool show "Show Sequence Viewer"
> sequence chain #7/A
Alignment identifier is 7/A
> select #7/A:33
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:33-135
819 atoms, 830 bonds, 103 residues, 1 model selected
> select #7/A:33
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:33-106
594 atoms, 599 bonds, 74 residues, 1 model selected
> select #7/A:33
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:33-112
634 atoms, 641 bonds, 80 residues, 1 model selected
> select #7/A:33
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:33-115
649 atoms, 656 bonds, 83 residues, 1 model selected
> select #7/A:33
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:33-62
254 atoms, 256 bonds, 30 residues, 1 model selected
> select #7/A:33
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:33-57
210 atoms, 212 bonds, 25 residues, 1 model selected
> mmaker #7 to #5
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7bdx, chain C (#5) with
ZCWPW1idr_ARMdimer_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_38557.pdb,
chain C (#7), sequence alignment score = 1049.6
RMSD between 210 pruned atom pairs is 0.672 angstroms; (across all 213 pairs:
0.782)
> view #5 clip false
No displayed objects specified.
> show #!5 target m
> view #5 clip false
> view matrix models
> #7,0.38841,0.91274,0.12662,136.83,0.17641,0.06122,-0.98241,181.76,-0.90444,0.40392,-0.13724,230.2
> select add #7
4539 atoms, 4604 bonds, 584 residues, 1 model selected
> select subtract #7
Nothing selected
> select #7/A:36
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:36-52
144 atoms, 145 bonds, 17 residues, 1 model selected
> label sel
> view matrix models
> #7,0.38841,0.91274,0.12662,138.59,0.17641,0.06122,-0.98241,183.35,-0.90444,0.40392,-0.13724,226.78
> view matrix models
> #7,0.38841,0.91274,0.12662,138.52,0.17641,0.06122,-0.98241,184.68,-0.90444,0.40392,-0.13724,230.11
> view matrix models
> #7,0.38841,0.91274,0.12662,138.35,0.17641,0.06122,-0.98241,183.75,-0.90444,0.40392,-0.13724,231.43
> select add #7
4539 atoms, 4604 bonds, 584 residues, 2 models selected
> select subtract #7
Nothing selected
> select #5/E
448 atoms, 442 bonds, 66 residues, 1 model selected
> label sel
> view matrix models
> #5,-0.86719,-0.4568,-0.19828,205.03,-0.49797,0.79334,0.3502,122.26,-0.0026691,0.40242,-0.91545,245.62
> select add #5
7434 atoms, 7385 bonds, 2 pseudobonds, 1110 residues, 3 models selected
> select subtract #5
Nothing selected
> ui tool show "Show Sequence Viewer"
> sequence chain #5/E
Alignment identifier is 5/E
> select #5/E:2312
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/E:2296-2312
131 atoms, 131 bonds, 17 residues, 1 model selected
> select add #5
7434 atoms, 7385 bonds, 2 pseudobonds, 1110 residues, 3 models selected
> select subtract #5
Nothing selected
> select #5/E:2306
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/E:2302-2306
37 atoms, 36 bonds, 5 residues, 1 model selected
> select #7/A:41
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #7/A:38-41
34 atoms, 33 bonds, 4 residues, 1 model selected
> open
> /Users/sz140275local/Downloads/fold_zcwpw2_hsf2bp/fold_zcwpw2_hsf2bp_model_0.cif
Chain information for fold_zcwpw2_hsf2bp_model_0.cif #8
---
Chain | Description
A | .
B C | .
Computing secondary structure
> select add #7
4539 atoms, 4604 bonds, 584 residues, 2 models selected
> select subtract #7
Nothing selected
> hide #!7 models
> hide #!5 models
> view #8 clip false
> color #8 bychain
> mmaker #8 to #5
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7bdx, chain C (#5) with fold_zcwpw2_hsf2bp_model_0.cif, chain B
(#8), sequence alignment score = 1052
RMSD between 208 pruned atom pairs is 0.657 angstroms; (across all 213 pairs:
0.799)
> view #5 clip false
No displayed objects specified.
> show #!5 target m
> select add #5
7434 atoms, 7385 bonds, 2 pseudobonds, 1110 residues, 3 models selected
> show #!5 target m
> view #5 clip false
> select subtract #5
Nothing selected
> select add #5
7434 atoms, 7385 bonds, 2 pseudobonds, 1110 residues, 3 models selected
> view matrix models
> #5,-0.86719,-0.4568,-0.19828,205.93,-0.49797,0.79334,0.3502,120.58,-0.0026691,0.40242,-0.91545,245.72
> select subtract #5
Nothing selected
> select add #5
7434 atoms, 7385 bonds, 2 pseudobonds, 1110 residues, 3 models selected
> view matrix models
> #5,-0.86719,-0.4568,-0.19828,213.03,-0.49797,0.79334,0.3502,112.79,-0.0026691,0.40242,-0.91545,246.87
> view matrix models
> #5,-0.86719,-0.4568,-0.19828,205.33,-0.49797,0.79334,0.3502,120.04,-0.0026691,0.40242,-0.91545,246.3
> view matrix models
> #5,-0.86719,-0.4568,-0.19828,205.33,-0.49797,0.79334,0.3502,120.92,-0.0026691,0.40242,-0.91545,245.8
> select subtract #5
Nothing selected
> close #8#1-7
> open
> /Users/sz140275local/Downloads/fold_zcwpw2_hsf2bp/fold_zcwpw2_hsf2bp_model_0.cif
Chain information for fold_zcwpw2_hsf2bp_model_0.cif #1
---
Chain | Description
A | .
B C | .
Computing secondary structure
> close
> open
> /Users/sz140275local/Downloads/fold_brh2_myst/fold_brh2_myst_model_0.cif
Chain information for fold_brh2_myst_model_0.cif #1
---
Chain | Description
A | .
B | .
Computing secondary structure
> open
> /Users/sz140275local/Downloads/Myst_BRC2_9deb6/predictions/Myst_BRC2/models/Myst_BRC2_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_97616.pdb
Chain information for
Myst_BRC2_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_97616.pdb #2
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> mmaker #1 to #2
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Myst_BRC2_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_97616.pdb,
chain B (#2) with fold_brh2_myst_model_0.cif, chain B (#1), sequence alignment
score = 1958.5
RMSD between 160 pruned atom pairs is 0.648 angstroms; (across all 394 pairs:
56.902)
> hide #2 models
> select #1
5188 atoms, 5286 bonds, 653 residues, 1 model selected
> color bfactor #1 palette alphafold
5188 atoms, 653 residues, atom bfactor range 14.1 to 98.7
> color bfactor #2 palette alphafold
5186 atoms, 653 residues, atom bfactor range 12.5 to 97.9
> select subtract #1
Nothing selected
> hide #1 models
> show #2 models
> color #2 bychain
> hide #2 models
> show #1 models
> color #1 bychain
> color bfactor #1 palette alphafold
5188 atoms, 653 residues, atom bfactor range 14.1 to 98.7
> color #1 bychain
> color bfactor #1 palette alphafold
5188 atoms, 653 residues, atom bfactor range 14.1 to 98.7
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> sequence chain #1/B
Alignment identifier is 1/B
> select #1/B:47
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/B:47-50
32 atoms, 31 bonds, 4 residues, 1 model selected
> select #1/B:138-139
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #1/B:138-146
75 atoms, 76 bonds, 9 residues, 1 model selected
> select #1/B:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:1-135
1019 atoms, 1036 bonds, 135 residues, 1 model selected
> hide sel cartoons
> color sel bychain
[Repeated 1 time(s)]
> select add #1
5188 atoms, 5286 bonds, 653 residues, 1 model selected
> color sel bychain
> color bfactor #1 palette alphafold
5188 atoms, 653 residues, atom bfactor range 14.1 to 98.7
> color sel bychain
> color bfactor #1 palette alphafold
5188 atoms, 653 residues, atom bfactor range 14.1 to 98.7
> select subtract #1
Nothing selected
> select #1/A:188
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:259
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:192-259
538 atoms, 545 bonds, 68 residues, 1 model selected
> hide sel cartoons
> select #1/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:1-6
57 atoms, 58 bonds, 6 residues, 1 model selected
> color sel bychain
> select add #1
5188 atoms, 5286 bonds, 653 residues, 1 model selected
> color sel bychain
> view matrix models
> #1,0.33487,-0.12445,-0.93401,-7.4476,-0.80193,0.48281,-0.35184,-5.6803,0.49474,0.86684,0.061879,-8.5074
> view matrix models
> #1,0.33487,-0.12445,-0.93401,-9.3257,-0.80193,0.48281,-0.35184,2.7441,0.49474,0.86684,0.061879,-8.0506
> select #1
5188 atoms, 5286 bonds, 653 residues, 1 model selected
> show sel cartoons
> undo
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for fold_brh2_myst_model_0.cif_A SES surface #1.1: minimum,
-23.03, mean -4.12, maximum 9.12
Coulombic values for fold_brh2_myst_model_0.cif_B SES surface #1.2: minimum,
-12.84, mean 1.69, maximum 25.66
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel surfaces
[Repeated 1 time(s)]
> coulombic sel
Coulombic values for fold_brh2_myst_model_0.cif_A SES surface #1.1: minimum,
-23.03, mean -4.12, maximum 9.12
Coulombic values for fold_brh2_myst_model_0.cif_B SES surface #1.2: minimum,
-12.84, mean 1.69, maximum 25.66
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic sel
Coulombic values for fold_brh2_myst_model_0.cif_A SES surface #1.1: minimum,
-23.03, mean -4.12, maximum 9.12
Coulombic values for fold_brh2_myst_model_0.cif_B SES surface #1.2: minimum,
-12.84, mean 1.69, maximum 25.66
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel surfaces
> select #1
5188 atoms, 5286 bonds, 653 residues, 1 model selected
> show sel cartoons
> undo
> open
> /Users/sz140275local/Downloads/fold_brca2_spat22/fold_brca2_spat22_model_0.cif
Chain information for fold_brca2_spat22_model_0.cif #3
---
Chain | Description
A | .
B | .
Computing secondary structure
> hide #!1 models
> select subtract #1
2 models selected
> select #3/A
2902 atoms, 2962 bonds, 363 residues, 1 model selected
> hide sel cartoons
> mmaker #3/B to #1
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_brh2_myst_model_0.cif, chain B (#1) with
fold_brca2_spat22_model_0.cif, chain B (#3), sequence alignment score = 134.6
RMSD between 11 pruned atom pairs is 1.151 angstroms; (across all 122 pairs:
68.784)
> show #!1 models
> select add #3
12221 atoms, 12475 bonds, 1531 residues, 1 model selected
> select subtract #3
Nothing selected
> hide #!1 models
> select #3/B:915-1400
1972 atoms, 2006 bonds, 254 residues, 1 model selected
> hide sel cartoons
> view matrix models
> #3,0.98522,-0.11524,0.12675,-38.628,0.1099,-0.1424,-0.98369,-60.891,0.13141,0.98308,-0.12763,-42.651
> view matrix models
> #3,0.98522,-0.11524,0.12675,-20.811,0.1099,-0.1424,-0.98369,-75.905,0.13141,0.98308,-0.12763,-23.979
> select add #3
12221 atoms, 12475 bonds, 1531 residues, 1 model selected
> select subtract #3
Nothing selected
> hide #3 models
> show #!1 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> mmaker #3/B:228-914 to #1
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_brh2_myst_model_0.cif, chain B (#1) with
fold_brca2_spat22_model_0.cif, chain B (#3), sequence alignment score = 50.2
RMSD between 20 pruned atom pairs is 0.237 angstroms; (across all 23 pairs:
4.177)
> hide #!1 models
> hide #3 models
> show #!1 models
> show #3 models
> hide #3 models
> show #3 models
> hide #!1 models
> select #3/B:1-22!
Expected an objects specifier or a keyword
> select #3/B:1-228
1845 atoms, 1882 bonds, 228 residues, 1 model selected
> hide sel cartoons
> mmaker #3/B:228-556 #1/A
> matchmaker #3/B:228-556 #1/A
Missing required "to" argument
> show #!1 models
> mmaker #3/B:228-556 to #1/B
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_brh2_myst_model_0.cif, chain B (#1) with
fold_brca2_spat22_model_0.cif, chain B (#3), sequence alignment score = 50.2
RMSD between 20 pruned atom pairs is 0.237 angstroms; (across all 23 pairs:
4.177)
> mmaker #3/B:228-556 to #1/B
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_brh2_myst_model_0.cif, chain B (#1) with
fold_brca2_spat22_model_0.cif, chain B (#3), sequence alignment score = 50.2
RMSD between 20 pruned atom pairs is 0.237 angstroms; (across all 23 pairs:
4.177)
> view matrix models
> #3,0.301,-0.92979,0.21186,-48.674,-0.74443,-0.36795,-0.55716,-37.368,0.596,0.0099913,-0.80292,-32.751
> hide #!1 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> mmaker #3/B:228-556 to #2/B
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Myst_BRC2_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_97616.pdb,
chain B (#2) with fold_brca2_spat22_model_0.cif, chain B (#3), sequence
alignment score = 50.2
RMSD between 20 pruned atom pairs is 0.332 angstroms; (across all 23 pairs:
4.056)
> show #2 models
> view matrix models
> #3,0.31129,-0.9166,0.25088,-41.935,-0.71012,-0.39979,-0.57956,-45.992,0.63153,0.0022549,-0.77535,-27.68
> view matrix models
> #3,0.31129,-0.9166,0.25088,-54.534,-0.71012,-0.39979,-0.57956,-57.743,0.63153,0.0022549,-0.77535,-45.976
> view matrix models
> #3,0.31129,-0.9166,0.25088,-72.304,-0.71012,-0.39979,-0.57956,-83.833,0.63153,0.0022549,-0.77535,-79.858
> select add #3
12221 atoms, 12475 bonds, 1531 residues, 1 model selected
> select subtract #3
Nothing selected
> select add #1
5188 atoms, 5286 bonds, 653 residues, 1 model selected
> select add #2
10374 atoms, 10570 bonds, 1306 residues, 4 models selected
> select add #3
22595 atoms, 23045 bonds, 2837 residues, 5 models selected
> open 7bdx
7bdx title:
Armadillo domain of HSF2BP in complex with BRCA2 peptide [more info...]
Chain information for 7bdx #4
---
Chain | Description | UniProt
A B C D | Heat shock factor 2-binding protein | HSF2B_HUMAN 122-334
E F | Breast cancer type 2 susceptibility protein | BRCA2_HUMAN 2291-2343
Non-standard residues in 7bdx #4
---
MG — magnesium ion
> select subtract #1
17407 atoms, 17759 bonds, 2184 residues, 4 models selected
> select subtract #2
12221 atoms, 12475 bonds, 1531 residues, 1 model selected
> select subtract #3
Nothing selected
> hide #2 models
> hide #3 models
> hide #!4 atoms
> show #!4 cartoons
> ui tool show "Show Sequence Viewer"
> sequence chain #4/F
Alignment identifier is 4/F
> select #4/F:2308
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/F:2308
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/F:2303
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/F:2303
6 atoms, 5 bonds, 1 residue, 1 model selected
> style sel stick
Changed 6 atom styles
> select #4/F:2307
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/F:2307
6 atoms, 5 bonds, 1 residue, 1 model selected
> style sel stick
Changed 6 atom styles
> show sel atoms
> select #4/F:2303
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/F:2303
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select #4/F:2309
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/F:2309-2310
13 atoms, 12 bonds, 2 residues, 1 model selected
> show sel atoms
> view matrix models #4,1,0,0,-14.296,0,1,0,10.173,0,0,1,-2.0796
> style sel stick
Changed 13 atom styles
> color sel red
> style sel sphere
Changed 13 atom styles
> select #4/F:2306-2307
11 atoms, 10 bonds, 2 residues, 1 model selected
> select #4/F:2306-2307
11 atoms, 10 bonds, 2 residues, 1 model selected
> select #4/F:2307
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/F:2307
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 6 atom styles
> color sel red
> select #4/F:2303
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/F:2303
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 6 atom styles
> color sel red
> select #4/D
1603 atoms, 1604 bonds, 233 residues, 1 model selected
> coulombic sel
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
7bdx #4/D ALA 121
7bdx #4/D GLN 173
7bdx #4/D GLU 174
7bdx #4/D LEU 175
7bdx #4/D PHE 296
7bdx #4/D ARG 297
7bdx #4/D SER 298
7bdx #4/D ARG 315
7bdx #4/D LEU 327
7bdx #4/D GLU 331
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 7bdx_D SES surface #4.2: minimum, -19.52, mean -2.41,
maximum 13.54
To also show corresponding color key, enter the above coulombic command and
add key true
> view matrix models #4,1,0,0,-29.844,0,1,0,16.522,0,0,1,-7.8195
> style sel stick
Changed 1603 atom styles
> style sel stick
Changed 1603 atom styles
> select add #4
7434 atoms, 7385 bonds, 2 pseudobonds, 1110 residues, 3 models selected
> style sel stick
Changed 7434 atom styles
> select subtract #4
1 model selected
> select #4/F:2309
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/F:2309
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/F:2307
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/F:2306-2307
11 atoms, 10 bonds, 2 residues, 1 model selected
> select #4/F:2309
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/F:2309
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/F:2310
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/F:2310
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/B
1673 atoms, 1653 bonds, 1 pseudobond, 257 residues, 2 models selected
> coulombic sel
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
7bdx #4/B ALA 121 CB
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 7bdx_B SES surface #4.3: minimum, -18.08, mean -2.65,
maximum 8.50
To also show corresponding color key, enter the above coulombic command and
add key true
> view matrix models #4,1,0,0,-17.975,0,1,0,11.313,0,0,1,-9.6789
> transparency sel 50
> open
> /Users/sz140275local/Downloads/fold_brca2_plk1/fold_brca2_plk1_model_0.cif
Chain information for fold_brca2_plk1_model_0.cif #5
---
Chain | Description
A | .
B | .
Computing secondary structure
> hide #!4 models
> select add #4
7434 atoms, 7385 bonds, 2 pseudobonds, 1110 residues, 3 models selected
> select subtract #4
2 models selected
> open 6GY2
6gy2 title:
Crystal structure of human Plk1-PBD in complex with WSSSLATPPTLSSpTVLI
phosphopeptide from BRCA2 [more info...]
Chain information for 6gy2 #6
---
Chain | Description | UniProt
A B | Serine/threonine-protein kinase PLK1 | PLK1_HUMAN 365-603
C D | Phosphopeptide of BRCA2 |
Non-standard residues in 6gy2 #6
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
6gy2 mmCIF Assemblies
---
1| software_defined_assembly
2| software_defined_assembly
> mmaker #5 to #6
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6gy2, chain B (#6) with fold_brca2_plk1_model_0.cif, chain B (#5),
sequence alignment score = 1188.3
RMSD between 216 pruned atom pairs is 0.519 angstroms; (across all 224 pairs:
1.056)
> select #6/A
1834 atoms, 1861 bonds, 235 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #6/D
89 atoms, 88 bonds, 14 residues, 1 model selected
> hide sel cartoons
> select add #6
3842 atoms, 3897 bonds, 495 residues, 1 model selected
> hide #5 models
> select subtract #6
Nothing selected
> select #6/C
88 atoms, 88 bonds, 13 residues, 1 model selected
> color sel green
> select add #6
3842 atoms, 3897 bonds, 495 residues, 1 model selected
> select subtract #6
Nothing selected
> show #5 models
> select #5/A
265 atoms, 267 bonds, 33 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #5/A
Alignment identifier is 5/A
> select #5/A:30
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #5/A:30
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> view matrix models
> #5,-0.95566,-0.26059,-0.13714,-21.364,-0.030473,0.55072,-0.83413,-19.947,0.29289,-0.79297,-0.53424,28.29
> select add #5
2391 atoms, 2435 bonds, 296 residues, 1 model selected
> select subtract #5
Nothing selected
> select #6/C:207
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> hide #5 models
> hide #6 models
> select add #6
3842 atoms, 3897 bonds, 495 residues, 1 model selected
> show #!4 models
> select subtract #6
Nothing selected
> view #6 clip false
> select add #4
7434 atoms, 7385 bonds, 2 pseudobonds, 1110 residues, 2 models selected
> show #6 target m
> hide #6 models
> show #!4 target m
> view #4 clip false
> select subtract #4
2 models selected
> hide #!4 models
> show #!1 models
> show #!4 target m
> hide #!4 models
> select add #1
5188 atoms, 5286 bonds, 653 residues, 1 model selected
> show #!1 target m
> view #1 clip false
> select subtract #1
2 models selected
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> sequence chain #1/B
Alignment identifier is 1/B
> select #1/B:136
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/B:136-138
29 atoms, 29 bonds, 3 residues, 1 model selected
> select #1/B:136
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/B:136-356
1796 atoms, 1828 bonds, 221 residues, 1 model selected
> select #1/B:136
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/B:136-394
2124 atoms, 2165 bonds, 259 residues, 1 model selected
> select #1/A:178
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:178-232
423 atoms, 426 bonds, 55 residues, 1 model selected
> select #1/A:259
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A
2045 atoms, 2084 bonds, 259 residues, 1 model selected
> select #1/A:197
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:191-197
43 atoms, 42 bonds, 7 residues, 1 model selected
> select #1/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:1-191
1507 atoms, 1538 bonds, 191 residues, 1 model selected
> open
> /Users/sz140275local/Downloads/fold_protsimer/fold_protsimer_model_0.cif
Chain information for fold_protsimer_model_0.cif #7
---
Chain | Description
A B | .
Computing secondary structure
> hide #!1 models
> select add #1
5188 atoms, 5286 bonds, 653 residues, 2 models selected
> select subtract #1
2 models selected
> select #7/A
2214 atoms, 2260 bonds, 277 residues, 1 model selected
> color sel lime
> select add #7
4428 atoms, 4520 bonds, 554 residues, 1 model selected
> select subtract #7
Nothing selected
> select #7/B
2214 atoms, 2260 bonds, 277 residues, 1 model selected
> color bfactor #7/B palette alphafold
2214 atoms, 277 residues, atom bfactor range 20.2 to 97.4
> select add #7
4428 atoms, 4520 bonds, 554 residues, 1 model selected
> select subtract #7
Nothing selected
> select #1/A:195
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:195-254
477 atoms, 483 bonds, 60 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #7/A
Alignment identifier is 7/A
> select #7/A:251-277
226 atoms, 230 bonds, 27 residues, 1 model selected
> select #7/A:198-277
623 atoms, 640 bonds, 80 residues, 1 model selected
> view matrix models #7,1,0,0,-12.479,0,1,0,-6.7066,0,0,1,-23.359
> view matrix models #7,1,0,0,12.034,0,1,0,-10.279,0,0,1,2.7897
> view matrix models #7,1,0,0,26.561,0,1,0,-12.856,0,0,1,43.524
> view matrix models #7,1,0,0,31.721,0,1,0,-20.189,0,0,1,28.966
> select #7/B:83
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/B:80
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #7/A:80
8 atoms, 7 bonds, 1 residue, 1 model selected
> color #7/B pinlk
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #7/B pink
> view matrix models #7,1,0,0,6.1539,0,1,0,-29.134,0,0,1,13.662
> open /Users/sz140275local/Downloads/AF-Q86WS4-F1-model_v4.pdb
AF-Q86WS4-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for uncharacterized protein C12ORF40
(Q86WS4) [more info...]
Chain information for AF-Q86WS4-F1-model_v4.pdb #8
---
Chain | Description | UniProt
A | uncharacterized protein C12ORF40 | CL040_HUMAN 1-652
Computing secondary structure
> hide #7 models
> select add #7
4428 atoms, 4520 bonds, 554 residues, 1 model selected
> select subtract #7
Nothing selected
> color bfactor #7/ palette alphafold
> color byattribute bfactor #7/ palette alphafold
Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword
> color bfactor #8 palette alphafold
5207 atoms, 652 residues, atom bfactor range 27.4 to 92.7
> hide #8 models
> show #7 models
> select #7/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #7/A:1-197
1591 atoms, 1619 bonds, 197 residues, 1 model selected
> select #7/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #7/A:1-81
620 atoms, 631 bonds, 81 residues, 1 model selected
> select #7/A:196-197
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #7/A:1-197
1591 atoms, 1619 bonds, 197 residues, 1 model selected
> open
> /Users/sz140275local/Downloads/fold_complexehei10foldnterdimer_redicnterdimer/fold_complexehei10foldnterdimer_redicnterdimer_model_0.cif
Chain information for
fold_complexehei10foldnterdimer_redicnterdimer_model_0.cif #9
---
Chain | Description
A B | .
C D | .
Computing secondary structure
> hide #7 models
> select add #7
4428 atoms, 4520 bonds, 554 residues, 1 model selected
> select subtract #7
Nothing selected
> ui tool show "Show Sequence Viewer"
> sequence chain #9/C
Alignment identifier is 9/C
> select #9/C:100
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/C:63-100
314 atoms, 320 bonds, 38 residues, 1 model selected
> open
> /Users/sz140275local/Downloads/fold_complexehei10foldntershortdimer_redicnterdimer/fold_complexehei10foldntershortdimer_redicnterdimer_model_0.cif
Chain information for
fold_complexehei10foldntershortdimer_redicnterdimer_model_0.cif #10
---
Chain | Description
A B | .
C D | .
Computing secondary structure
> hide #9 models
> select add #9
4820 atoms, 4902 bonds, 594 residues, 1 model selected
> color #10 bychain
> view matrix models #9,1,0,0,27.223,0,1,0,11.668,0,0,1,1.7485
> view matrix models #9,1,0,0,59.533,0,1,0,28.672,0,0,1,5.8463
> view matrix models #9,1,0,0,75.016,0,1,0,35.933,0,0,1,7.2413
> color bfactor #10 palette alphafold
2510 atoms, 320 residues, atom bfactor range 18.5 to 98.1
> view matrix models #9,1,0,0,88.609,0,1,0,10.762,0,0,1,11.708
> ui mousemode right zoom
> ui tool show "Show Sequence Viewer"
> sequence chain #10/C
Alignment identifier is 10/C
> select clear
> select #10/C:19
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #10/C:13
7 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
[Repeated 3 time(s)]
> select #10/C:19
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #10/C:13
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #10/C:13-19
55 atoms, 56 bonds, 7 residues, 1 model selected
> select #10/C:24-25
15 atoms, 15 bonds, 2 residues, 1 model selected
> select #10/C:15-25
92 atoms, 93 bonds, 11 residues, 1 model selected
> open
> /Users/sz140275local/Downloads/MinComplex_cff0e/predictions/MinComplex/models/MinComplex_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_59653.pdb
Chain information for
MinComplex_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_59653.pdb
#11
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> hide #10 models
> select add #10
2510 atoms, 2556 bonds, 320 residues, 1 model selected
> select subtract #10
Nothing selected
> color #11 bychain
> select #11/A
620 atoms, 631 bonds, 81 residues, 1 model selected
> color sel lime
> select add #11
964 atoms, 978 bonds, 124 residues, 1 model selected
> select subtract #11
Nothing selected
> color bfactor #11/B palette alphafold
344 atoms, 43 residues, atom bfactor range 26.5 to 82.9
> ui tool show "Show Sequence Viewer"
> sequence chain #11/B
Alignment identifier is 11/B
> select #11/B:27
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #11/B:27-43
142 atoms, 143 bonds, 17 residues, 1 model selected
> hide #11 models
> select add #11
964 atoms, 978 bonds, 124 residues, 1 model selected
> show #10 models
> select subtract #11
Nothing selected
> color #10 bychain
> hide #10 models
> show #11 models
> select #11/B:2
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #11/B:2
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #11/B:21-22
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #11/B:21-24
33 atoms, 32 bonds, 4 residues, 1 model selected
> select #11/B:2-3
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #11/B:2-3
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #11/B:21-22
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #11/B:21-23
24 atoms, 23 bonds, 3 residues, 1 model selected
> select #11/B:24
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #11/B:22-24
27 atoms, 26 bonds, 3 residues, 1 model selected
> show sel atoms
> select #11/B:9
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #11/B:9
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #11/A
620 atoms, 631 bonds, 81 residues, 1 model selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for
MinComplex_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_59653.pdb_A
SES surface #11.1: minimum, -12.42, mean -0.56, maximum 9.15
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!11 models
> select add #11
964 atoms, 978 bonds, 124 residues, 2 models selected
> select subtract #11
1 model selected
> show #10 models
> mmaker #11/B to #10
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_complexehei10foldntershortdimer_redicnterdimer_model_0.cif,
chain C (#10) with
MinComplex_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_59653.pdb,
chain B (#11), sequence alignment score = 92.1
RMSD between 7 pruned atom pairs is 1.211 angstroms; (across all 24 pairs:
9.433)
> show #!11 models
> ui mousemode right translate
> hide #10 models
> show #10 models
> hide #10#!11 surfaces
[Repeated 1 time(s)]
> hide #10 models
> show #10 models
> hide #10 models
> show #10 models
> mmaker #11/B to #10/A
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_complexehei10foldntershortdimer_redicnterdimer_model_0.cif,
chain A (#10) with
MinComplex_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_59653.pdb,
chain B (#11), sequence alignment score = 23
RMSD between 19 pruned atom pairs is 0.314 angstroms; (across all 21 pairs:
2.062)
> select add #11
964 atoms, 978 bonds, 124 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.45417,0.17343,-0.87387,-7.6896,-0.21821,-0.92934,-0.29784,-6.1638,-0.86378,0.32596,-0.38423,-6.7588
> view matrix models
> #11,0.45417,0.17343,-0.87387,-9.0774,-0.21821,-0.92934,-0.29784,-10.446,-0.86378,0.32596,-0.38423,-4.0281
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.75776,0.22696,-0.61179,-11.227,-0.17588,-0.83183,-0.52643,-8.4392,-0.62838,0.50651,-0.59041,-2.1338
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.75776,0.22696,-0.61179,-11.483,-0.17588,-0.83183,-0.52643,-13.357,-0.62838,0.50651,-0.59041,-6.6171
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.92185,-0.22361,-0.31652,-10.061,-0.35913,-0.79989,-0.48084,-15.057,-0.14566,0.55693,-0.81769,-2.1088
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.92185,-0.22361,-0.31652,-7.9745,-0.35913,-0.79989,-0.48084,-11.144,-0.14566,0.55693,-0.81769,-9.1072
> view matrix models
> #11,0.92185,-0.22361,-0.31652,-4.7457,-0.35913,-0.79989,-0.48084,-12.185,-0.14566,0.55693,-0.81769,-7.597
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.58872,-0.34667,-0.73023,-0.3068,-0.62533,-0.76776,-0.13967,-17.771,-0.51222,0.53886,-0.66878,-10.926
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.58872,-0.34667,-0.73023,-2.8607,-0.62533,-0.76776,-0.13967,-18.042,-0.51222,0.53886,-0.66878,-11.237
> view matrix models
> #11,0.58872,-0.34667,-0.73023,-5.4691,-0.62533,-0.76776,-0.13967,-10.92,-0.51222,0.53886,-0.66878,-10.008
> view matrix models
> #11,0.58872,-0.34667,-0.73023,-5.9244,-0.62533,-0.76776,-0.13967,-9.4818,-0.51222,0.53886,-0.66878,-9.2632
> view matrix models
> #11,0.58872,-0.34667,-0.73023,-7.0168,-0.62533,-0.76776,-0.13967,-9.3366,-0.51222,0.53886,-0.66878,-9.0932
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.60946,-0.49396,-0.62012,-6.8682,-0.74675,-0.62039,-0.23974,-10.081,-0.2663,0.60919,-0.74697,-7.65
> select subtract #11
1 model selected
> ui mousemode right zoom
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #10 models
> show #7 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> select add #11
964 atoms, 978 bonds, 124 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.60946,-0.49396,-0.62012,-5.0789,-0.74675,-0.62039,-0.23974,-12.86,-0.2663,0.60919,-0.74697,-19.599
> view matrix models
> #11,0.60946,-0.49396,-0.62012,-10.025,-0.74675,-0.62039,-0.23974,-23.461,-0.2663,0.60919,-0.74697,-15.959
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.5001,-0.78903,0.35683,-24.114,-0.86467,0.47752,-0.15596,-35.081,-0.04734,-0.38654,-0.92106,-3.7318
> view matrix models
> #11,-0.86805,-0.37548,0.32482,-29.272,-0.49639,0.64332,-0.58287,-29.814,0.0098938,-0.6672,-0.74482,-2.9684
> view matrix models
> #11,-0.81472,0.47872,0.32719,-36.883,0.035261,0.60413,-0.7961,-24.418,-0.57878,-0.63707,-0.50908,-8.8173
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.81472,0.47872,0.32719,-28.458,0.035261,0.60413,-0.7961,-19.19,-0.57878,-0.63707,-0.50908,-22.659
> view matrix models
> #11,-0.81472,0.47872,0.32719,-28.584,0.035261,0.60413,-0.7961,-12.041,-0.57878,-0.63707,-0.50908,-26.684
> view matrix models
> #11,-0.81472,0.47872,0.32719,-22.139,0.035261,0.60413,-0.7961,-19.132,-0.57878,-0.63707,-0.50908,-24.143
> view matrix models
> #11,-0.81472,0.47872,0.32719,-30.491,0.035261,0.60413,-0.7961,-28.714,-0.57878,-0.63707,-0.50908,-16.793
> view matrix models
> #11,-0.81472,0.47872,0.32719,-29.135,0.035261,0.60413,-0.7961,-23.604,-0.57878,-0.63707,-0.50908,-14.034
> ui mousemode right translate
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.75974,0.46914,-0.45023,-19.602,0.28528,-0.38171,-0.87915,-12.396,-0.5843,-0.79637,0.15616,-20.458
> view matrix models
> #11,-0.34315,0.54622,-0.76413,-14.628,0.49887,-0.58332,-0.64099,-12.349,-0.79585,-0.60116,-0.07233,-20.551
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.34315,0.54622,-0.76413,-15.814,0.49887,-0.58332,-0.64099,-18.705,-0.79585,-0.60116,-0.07233,-21.537
> view matrix models
> #11,-0.34315,0.54622,-0.76413,-16.508,0.49887,-0.58332,-0.64099,-21.067,-0.79585,-0.60116,-0.07233,-22.136
> view matrix models
> #11,-0.34315,0.54622,-0.76413,-16.657,0.49887,-0.58332,-0.64099,-22.026,-0.79585,-0.60116,-0.07233,-22.257
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.92723,0.31326,-0.2052,-23.889,0.30484,0.31311,-0.89946,-28.115,-0.21751,-0.89657,-0.38582,-13.105
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.92723,0.31326,-0.2052,-27.671,0.30484,0.31311,-0.89946,-22.477,-0.21751,-0.89657,-0.38582,-16.682
> view matrix models
> #11,-0.92723,0.31326,-0.2052,-25.736,0.30484,0.31311,-0.89946,-19.062,-0.21751,-0.89657,-0.38582,-22.092
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.57665,0.13065,-0.80647,-9.8366,0.040993,0.98126,0.18828,-39.291,0.81596,-0.14163,0.56049,-35.303
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.57665,0.13065,-0.80647,-10.183,0.040993,0.98126,0.18828,-29.954,0.81596,-0.14163,0.56049,-31.515
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.9282,-0.34226,0.14594,-15.432,0.23645,0.84545,0.47887,-31.216,-0.28728,-0.40998,0.86567,-37.883
> view matrix models
> #11,0.91745,0.007446,0.39777,-21.666,0.018868,0.99789,-0.062197,-27.252,-0.3974,0.064568,0.91537,-43.345
> view matrix models
> #11,0.90846,0.060592,0.41355,-22.382,-0.0036715,0.99055,-0.13707,-26.407,-0.41795,0.123,0.9001,-43.798
> view matrix models
> #11,0.90063,0.10119,0.42265,-22.899,-0.019506,0.98095,-0.1933,-25.73,-0.43416,0.16584,0.88544,-44.094
> view matrix models
> #11,0.88244,0.18279,0.43347,-23.862,-0.047836,0.95151,-0.30386,-24.288,-0.46799,0.2474,0.84839,-44.565
> view matrix models
> #11,0.12024,0.89703,0.42531,-33.926,-0.81638,0.33311,-0.47177,-20.27,-0.56486,-0.29049,0.77237,-39.191
> view matrix models
> #11,0.23492,0.92442,0.30042,-32.159,-0.90485,0.32088,-0.2798,-22.845,-0.35505,-0.2061,0.91184,-40.62
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.23492,0.92442,0.30042,-28.316,-0.90485,0.32088,-0.2798,-20.032,-0.35505,-0.2061,0.91184,-11.358
> view matrix models
> #11,0.23492,0.92442,0.30042,-21.791,-0.90485,0.32088,-0.2798,-20.582,-0.35505,-0.2061,0.91184,-15.337
> view matrix models
> #11,0.23492,0.92442,0.30042,-22.627,-0.90485,0.32088,-0.2798,-15.199,-0.35505,-0.2061,0.91184,-13.084
> view matrix models
> #11,0.23492,0.92442,0.30042,-23.105,-0.90485,0.32088,-0.2798,-14.499,-0.35505,-0.2061,0.91184,-13.587
> select subtract #11
1 model selected
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> select #11/B:2-24,27-30
214 atoms, 213 bonds, 27 residues, 1 model selected
> select #11/A
620 atoms, 631 bonds, 81 residues, 1 model selected
> coulombic sel
Coulombic values for
MinComplex_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_59653.pdb_A
SES surface #11.1: minimum, -12.42, mean -0.56, maximum 9.15
To also show corresponding color key, enter the above coulombic command and
add key true
> select add #11
964 atoms, 978 bonds, 124 residues, 2 models selected
> select subtract #11
1 model selected
> select #11/B:4
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #11/B:4
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select #11/B:7
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #11/B:7
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select #11/B:20
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #11/B:20
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select #11/B:2-24,27-30
214 atoms, 213 bonds, 27 residues, 1 model selected
> select #11/B:28
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #11/B:28
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #11/B:7
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #11/B:7
6 atoms, 5 bonds, 1 residue, 1 model selected
> open
> /Users/sz140275local/Downloads/Hop1_Mnd1_8398f/predictions/Hop1_Mnd1/models/Hop1_Mnd1_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_82003.pdb
Chain information for
Hop1_Mnd1_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_82003.pdb #12
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> select add #11
964 atoms, 978 bonds, 124 residues, 1 model selected
> select subtract #11
1 model selected
> hide #!11 models
> ui mousemode right zoom
> ui tool show "Show Sequence Viewer"
> sequence chain #12/A
Alignment identifier is 12/A
> sequence chain #12/B
Alignment identifier is 12/B
> select #12/B:72
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #12/B:72-75
37 atoms, 40 bonds, 4 residues, 1 model selected
> show sel atoms
> select #12/B:195
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #12/B:195-198
30 atoms, 31 bonds, 4 residues, 1 model selected
> show sel atoms
> select #12/B:187
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/B:187-205
163 atoms, 166 bonds, 19 residues, 1 model selected
> ui mousemode right translate
> select #12/B:185
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #12/B:185-205
178 atoms, 182 bonds, 21 residues, 1 model selected
> hide #12 models
> select add #12
3412 atoms, 3460 bonds, 422 residues, 1 model selected
> select subtract #12
Nothing selected
> show #!11 models
> ui mousemode right zoom
> ui mousemode right translate
> ui tool show "Show Sequence Viewer"
> sequence chain #11/B
Alignment identifier is 11/B
> select #11/B:20
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #11/B:20
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel green
> select add #11
964 atoms, 978 bonds, 124 residues, 1 model selected
> select subtract #11
1 model selected
> transparency #11.1 50
> open
> /Users/sz140275local/Downloads/MinComplexP_6bcbe/predictions/MinComplexP/models/MinComplexP_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_14081.pdb
Chain information for
MinComplexP_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_14081.pdb
#13
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> mmaker #12 to #11
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
MinComplex_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_59653.pdb,
chain B (#11) with
Hop1_Mnd1_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_82003.pdb,
chain B (#12), sequence alignment score = 46
RMSD between 23 pruned atom pairs is 0.617 angstroms; (across all 42 pairs:
24.380)
> mmaker #12 to #11
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
MinComplex_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_59653.pdb,
chain B (#11) with
Hop1_Mnd1_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_82003.pdb,
chain B (#12), sequence alignment score = 46
RMSD between 23 pruned atom pairs is 0.617 angstroms; (across all 42 pairs:
24.380)
> mmaker #13 to #11
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
MinComplex_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_59653.pdb,
chain A (#11) with
MinComplexP_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_14081.pdb,
chain A (#13), sequence alignment score = 425.3
RMSD between 80 pruned atom pairs is 0.615 angstroms; (across all 81 pairs:
0.655)
> hide #!11 models
> show #!11 models
> hide #!11 models
> color #13/A green
> select #13/A
620 atoms, 631 bonds, 81 residues, 1 model selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for
MinComplexP_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_14081.pdb_A
SES surface #13.1: minimum, -14.04, mean -0.47, maximum 9.17
To also show corresponding color key, enter the above coulombic command and
add key true
> color bfactor #113B palette alphafold
> color byattribute bfactor #113B palette alphafold
Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword
> color bfactor #13/B palette alphafold
347 atoms, 43 residues, atom bfactor range 25.8 to 83.8
> select add #13
967 atoms, 981 bonds, 124 residues, 2 models selected
> select #13/B:20
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel green
> select add #13
967 atoms, 981 bonds, 124 residues, 1 model selected
> select subtract #13
1 model selected
> hide #!13 models
> show #!13 models
> open
> /Users/sz140275local/Downloads/fold_complexehei10foldntershort_redicnterb_phospho/fold_complexehei10foldntershort_redicnterb_phospho_model_0.cif
Chain information for
fold_complexehei10foldntershort_redicnterb_phospho_model_0.cif #14
---
Chain | Description
A | .
B | .
Computing secondary structure
> mmaker #14 to #13
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
MinComplexP_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_14081.pdb,
chain A (#13) with
fold_complexehei10foldntershort_redicnterb_phospho_model_0.cif, chain A (#14),
sequence alignment score = 368.9
RMSD between 60 pruned atom pairs is 0.906 angstroms; (across all 81 pairs:
5.001)
> hide #!13 models
> select #14/B:20
10 atoms, 9 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> select add #14
970 atoms, 984 bonds, 124 residues, 1 model selected
> select subtract #14
Nothing selected
> select #14/A
621 atoms, 632 bonds, 81 residues, 1 model selected
> color sel green
> select add #14
970 atoms, 984 bonds, 124 residues, 1 model selected
> select subtract #14
Nothing selected
> show #!13 models
> hide #14#!13 surfaces
> hide #!13 models
> coulombic #14
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue SEP (net charge -1) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/dd/q54xxd8s6h7cd69lnrz0_1bc0000gn/T/tmpb2ugs2q5/ante.in.mol2 -fi
mol2 -o
/var/folders/dd/q54xxd8s6h7cd69lnrz0_1bc0000gn/T/tmpb2ugs2q5/ante.out.mol2 -fo
mol2 -c bcc -nc -1 -j 5 -s 2 -dr n
(SEP) ``
(SEP) `Welcome to antechamber 20.0: molecular input file processor.`
(SEP) ``
(SEP) `Info: Finished reading file
(/var/folders/dd/q54xxd8s6h7cd69lnrz0_1bc0000gn/T/tmpb2ugs2q5/ante.in.mol2);
atoms read (27), bonds read (26).`
(SEP) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(SEP) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(SEP) ``
(SEP) ``
(SEP) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(SEP) `Info: Total number of electrons: 126; net charge: -1`
(SEP) ``
(SEP) `Running: /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
(SEP) ``
(SEP) `Running: /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/am1bcc
-i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`
(SEP) ``
(SEP) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(SEP) ``
Charges for residue SEP determined
Coulombic values for
fold_complexehei10foldntershort_redicnterb_phospho_model_0.cif_A SES surface
#14.1: minimum, -11.49, mean -0.49, maximum 10.98
Coulombic values for
fold_complexehei10foldntershort_redicnterb_phospho_model_0.cif_B SES surface
#14.2: minimum, -9.14, mean 1.34, maximum 11.25
To also show corresponding color key, enter the above coulombic command and
add key true
> select #14/B
349 atoms, 352 bonds, 43 residues, 1 model selected
> hide sel surfaces
> show sel atoms
> label residues
> label sel
> open /Users/sz140275local/Downloads/AF-Q9Y620-F1-model_v4.pdb
AF-Q9Y620-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for DNA repair and recombination protein
RAD54B (Q9Y620) [more info...]
Chain information for AF-Q9Y620-F1-model_v4.pdb #15
---
Chain | Description | UniProt
A | DNA repair and recombination protein RAD54B | RA54B_HUMAN 1-910
Computing secondary structure
> hide #!14 models
> select add #14
970 atoms, 984 bonds, 124 residues, 3 models selected
> select subtract #14
2 models selected
> color bfactor #15 palette alphafold
7236 atoms, 910 residues, atom bfactor range 23.5 to 96.1
> ui tool show "Show Sequence Viewer"
> sequence chain #15/A
Alignment identifier is 15/A
> select #15/A:228
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #15/A:228-231
32 atoms, 33 bonds, 4 residues, 1 model selected
> show sel atoms
> open "/Users/sz140275local/Downloads/AF-Q9Y620-F1-model_v4 (1).pdb"
AF-Q9Y620-F1-model_v4 (1).pdb title:
Alphafold monomer V2.0 prediction for DNA repair and recombination protein
RAD54B (Q9Y620) [more info...]
Chain information for AF-Q9Y620-F1-model_v4 (1).pdb #16
---
Chain | Description | UniProt
A | DNA repair and recombination protein RAD54B | RA54B_HUMAN 1-910
Computing secondary structure
> hide #15 models
> select add #15
7236 atoms, 7387 bonds, 910 residues, 1 model selected
> select subtract #15
Nothing selected
> close #16
> show #15 models
> ui tool show "Show Sequence Viewer"
> sequence chain #15/A
Alignment identifier is 15/A
> select #15/A:26-27
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #15/A:26-225
1549 atoms, 1577 bonds, 200 residues, 1 model selected
> select clear
> select #15/A:123
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #15/A:197
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #15/A:207
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #15/A:208
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #15/A:123
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #15/A:123-211
705 atoms, 718 bonds, 89 residues, 1 model selected
> select #15/A:207
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #15/A:123-207
673 atoms, 685 bonds, 85 residues, 1 model selected
> select #15/A:251
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #15/A:251-803
4433 atoms, 4525 bonds, 553 residues, 1 model selected
> select #15/A:26
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #15/A:26-225
1549 atoms, 1577 bonds, 200 residues, 1 model selected
> select #15/A:476
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #15/A:476-479
33 atoms, 34 bonds, 4 residues, 1 model selected
> open
> /Users/sz140275local/Documents/Collab_Fred_Baudat/RAD54BnterDMC1_85bb9/predictions/RAD54BnterDMC1/models/RAD54BnterDMC1_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_29694.pdb
Chain information for
RAD54BnterDMC1_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_29694.pdb
#16
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> hide #15 models
> select add #15
7236 atoms, 7387 bonds, 910 residues, 1 model selected
> select subtract #15
Nothing selected
> select #6/B
1831 atoms, 1860 bonds, 233 residues, 1 model selected
> select #16/B
2646 atoms, 2688 bonds, 340 residues, 1 model selected
> color bfactor #16/B palette alphafold
2646 atoms, 340 residues, atom bfactor range 32.7 to 98.9
> color bfactor #16/A palette alphafold
387 atoms, 50 residues, atom bfactor range 15.1 to 89
> open
> /Users/sz140275local/Documents/Collab_Fred_Baudat/RAD54B200DMC1_1afb7/predictions/RAD54B200DMC1/models/RAD54B200DMC1_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_60027.pdb
Chain information for
RAD54B200DMC1_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_60027.pdb
#17
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> mmaker #16 to #17
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
RAD54B200DMC1_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_60027.pdb,
chain B (#17) with
RAD54BnterDMC1_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_29694.pdb,
chain B (#16), sequence alignment score = 1724.4
RMSD between 329 pruned atom pairs is 0.225 angstroms; (across all 340 pairs:
0.771)
> color bfactor #17/A palette alphafold
382 atoms, 50 residues, atom bfactor range 14.7 to 84.4
> select add #16
3033 atoms, 3083 bonds, 390 residues, 1 model selected
> select subtract #16
Nothing selected
> select #17/A:32
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #17/A:28
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #17/A:31
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #16/A:20
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #16/A:22
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #16/A:23
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #16/A:24
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 2 time(s)]
> open
> /Users/sz140275local/Downloads/RAD54BnterRAD51_aef71/predictions/RAD54BnterRAD51/models/RAD54BnterRAD51_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_85478.pdb
Chain information for
RAD54BnterRAD51_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_85478.pdb
#18
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> select add #16
3033 atoms, 3083 bonds, 390 residues, 1 model selected
> select subtract #16
Nothing selected
> mmaker #18 to #16
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
RAD54BnterDMC1_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_29694.pdb,
chain B (#16) with
RAD54BnterRAD51_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_85478.pdb,
chain B (#18), sequence alignment score = 1085.9
RMSD between 274 pruned atom pairs is 0.889 angstroms; (across all 336 pairs:
3.231)
> hide #16 models
> hide #17 models
> color bfactor #1<!/A palette alphafold
> color byattribute bfactor #1<!/A palette alphafold
Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword
> color bfactor #18/A palette alphafold
387 atoms, 50 residues, atom bfactor range 15.5 to 82.3
> show #17 models
> hide #17 models
> show #16 models
> select #18/A:23
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #18/A:22
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #18/A:20
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> open
> /Users/sz140275local/Downloads/RAD54B200RAD51_0825e/predictions/RAD54B200RAD51/models/RAD54B200RAD51_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_63869.pdb
Chain information for
RAD54B200RAD51_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_63869.pdb
#19
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> color bfactor #19/A palette alphafold
382 atoms, 50 residues, atom bfactor range 15.8 to 69.8
> mmaker #19 to #16
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
RAD54BnterDMC1_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_29694.pdb,
chain B (#16) with
RAD54B200RAD51_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_63869.pdb,
chain B (#19), sequence alignment score = 1075.2
RMSD between 287 pruned atom pairs is 0.863 angstroms; (across all 338 pairs:
2.588)
> select add #18
2975 atoms, 3020 bonds, 389 residues, 1 model selected
> hide #16 models
> show #17 models
> hide #18 models
> select subtract #18
Nothing selected
> select #19/A:32
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #19/A:35
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> hide #17 models
> ui tool show "Show Sequence Viewer"
> sequence chain #19/A
Alignment identifier is 19/A
> select #19/A:32
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #19/A:32-35
33 atoms, 33 bonds, 4 residues, 1 model selected
> show #17 models
> hide #17 models
> show #17 models
> close #2-3,5-10,12,15-19#1,4,11,13-14
> open
> /Users/sz140275local/Downloads/cryosparc_P26_J216_011_volume_map_sharp.mrc
Opened cryosparc_P26_J216_011_volume_map_sharp.mrc as #1, grid size
336,336,336, pixel 0.745, shown at level 0.0337, step 2, values float32
> open /Users/sz140275local/Downloads/cryosparc_P26_J216_011_volume_map.mrc
Opened cryosparc_P26_J216_011_volume_map.mrc as #2, grid size 336,336,336,
pixel 0.745, shown at level 0.0204, step 2, values float32
> open /Users/sz140275local/Downloads/J216_011_volume_map_ABCEF.pdb
Chain information for J216_011_volume_map_ABCEF.pdb #3
---
Chain | Description
A B C D E F | No description available
M N O P Q R | No description available
X | No description available
> hide #!2 models
> hide #!1 models
> hide atoms
> show cartoons
Computing secondary structure
> show #!2 models
> hide #!2 models
> show #!2 models
> transparency #2.1 50
> ui mousemode right zoom
> ui tool show "Show Sequence Viewer"
> hide #!2 models
> ui tool show "Show Sequence Viewer"
> sequence chain /O
Alignment identifier is 3/O
> select #3/X
360 atoms, 395 bonds, 18 residues, 1 model selected
> color sel black
> select add #3
15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 2 models selected
> select subtract #3
Nothing selected
> color #3/A,C,E,G,I royal blue
> select clear
[Repeated 1 time(s)]
> color #3/M,N,O,P,Q red
> color #3/F,D,B wheat
> lighting soft
> graphics silhouettes true width 2
> background white
Unknown command: background white
> cartoon style strand width 3 thickness 1
> cartoon style helix width 3 thickness 1
> cartoon style coil width 2 thickness 1.5
> cartoon style nucleic width 1.2 thickness 1.2 xsection section oval
Invalid "xsection" argument: Should be one of 'barbell', 'oval', 'piping',
'rectangle', 'round', or 'square'
> select #3/M,N,O,P,Q
275 atoms, 290 bonds, 35 residues, 1 model selected
> show sel atoms
> size #3/M,N,O,P,Q stickRadius 2
Changed 290 bond radii
> size #3/M,N,O,P,Q stickRadius 0.5
Changed 290 bond radii
> select add #3
15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 2 models selected
> select subtract #3
Nothing selected
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
> RAD54/FVdmc1BRCA2.tif" width 884 height 589 supersample 3
> show #!1 models
> surface dust #1 size 7.45
> transparency #1.1 50
> color zone #1 near #3 distance 4.47
> transparency #1.1 0
> transparency #1.1 50
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
> RAD54/FVdmc1BRCA2withMap.tif" width 884 height 589 supersample 3
> ui mousemode right translate
> ui mousemode right zoom
> hide #!3 models
> show #!3 models
> hide #!3 models
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> graphics silhouettes true width 1
> graphics silhouettes true width 3
> graphics silhouettes false width 3
> graphics silhouettes true width 3
> lighting
Intensity: 0
Direction: 0.577,-0.577,-0.577
Color: 100,100,100
Fill intensity: 0
Fill direction: -0.2,-0.2,-0.959
Fill color: 100,100,100
Ambient intensity: 1.5
Ambient color: 100,100,100
Depth cue: 0, start 0.5, end 1, color 100,100,100
Shadow: False (depth map size 2048, depth bias 0.005)
Multishadows: 64 (max 1024, depth map size 1024, depth bias 0.01)
> lighting simple
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> volume #!1 showOutlineBox true
> volume #!1 showOutlineBox false
> transparency #1.1 0
> transparency #1.1 50
> show #!3 models
> volume #1 level 0.02152
> volume #1 level 0.02422
> color zone #1 near #3 distance 4.47
> surface dust #1 size 7.45
> transparency #1.1 0
> transparency #1.1 50
> ui mousemode right translate
> volume #1 level 0.02692
> color zone #1 near #3 distance 4.47
> surface dust #1 size 7.45
> transparency #1.1 0
> transparency #1.1 50
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> hide #!3 models
> ui mousemode right zoom
> transparency #1.1 0
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> transparency #1.1 50
> transparency #1.1 0
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> transparency #1.1 50
> transparency #1.1 0
> transparency #1.1 50
> transparency #1.1 0
> show #!2 models
> hide #!1 models
> show #!3 models
> color zone #2 near #3 distance 4.47
> volume #2 level 0.01243
> surface dust #2 size 7.45
> transparency #2.1 0
> transparency #2.1 50
> transparency #2.1 0
> hide #!3 models
> volume #2 level 0.01409
Color zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 1 maps.
[Repeated 1 time(s)]
> show #!3 models
> color zone #2 near #3 distance 4.47
> hide #!3 models
> color #2 #fbffd180 models
> color #2 #ffeeef80 models
> color #2 #ffeef080 models
> color #2 #dccdcf80 models
> show #!3 models
> color zone #2 near #3 distance 4.47
> hide #!3 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
> RAD54/FVdmc1BRCA2zoom1.tif" width 884 height 589 supersample 3
> show #!3 models
> transparency #2.1 0
> transparency #2.1 50
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right zoom
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
> RAD54/FVdmc1BRCA2withMap2.tif" width 884 height 589 supersample 3
> ui mousemode right translate
> ui mousemode right zoom
> show #!1 models
> hide #!2 models
> transparency #1.1 50
> transparency #1.1 0
> transparency #1.1 50
> transparency #1.1 0
> transparency #1.1 50
> ui mousemode right translate
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!1 models
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
> RAD54/FVdmc1BRCA2withMapZ3.tif" width 884 height 589 supersample 3
> hide #!1 models
> label #3/O
> show #!1 models
> hide #!3 models
> show #!3 models
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right zoom
> select #3/O
55 atoms, 58 bonds, 7 residues, 1 model selected
> ~label sel residues
> select add #3
15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 2 models selected
> select subtract #3
Nothing selected
> ui mousemode right translate
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> ui mousemode right zoom
> ui mousemode right translate
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
> RAD54/BRCA2struct1.tif" width 884 height 589 supersample 3
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> volume #2 level 0.01143
> color zone #2 near #3 distance 4.47
> transparency #2.1 0
> transparency #2.1 50
> hide #!2 models
> select /D:85
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select /D:89
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select /D:85@CD2
1 atom, 1 residue, 1 model selected
> hide sel atoms
[Repeated 1 time(s)]
> select /D:85@CA
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select /D:85@CB
1 atom, 1 residue, 1 model selected
> select /D:85@CG
1 atom, 1 residue, 1 model selected
> select /D:85@CE2
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select /D:85@CB
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select /D:85@CG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select /D:85@CD1
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select /D:85@CZ
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select /D:85@CE1
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #3/C,D
4876 atoms, 4952 bonds, 2 pseudobonds, 628 residues, 2 models selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for J216_011_volume_map_ABCEF.pdb_C SES surface #3.2:
minimum, -26.80, mean -0.75, maximum 13.88
Coulombic values for J216_011_volume_map_ABCEF.pdb_D SES surface #3.3:
minimum, -27.43, mean -0.73, maximum 14.12
To also show corresponding color key, enter the above coulombic command and
add key true
> transparency sel 50
> select add #3
15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 4 models selected
> transparency sel 0
> transparency sel 50
> select /C:20@N
1 atom, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> transparency sel 0
> select add #3
15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 3 models selected
> select subtract #3
2 models selected
> select add #3
15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 2 models selected
> transparency sel 0
> transparency sel 50
> transparency sel 0
> transparency sel 50
> transparency sel 0
> transparency sel 50
> transparency sel 0
> transparency sel 50
> transparency sel 0
> select subtract #3
2 models selected
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
> RAD54/BRCA2elec1.tif" width 884 height 589 supersample 3
> hide surfaces
> ui mousemode right zoom
> ui mousemode right translate
> select #3/A
2438 atoms, 2476 bonds, 1 pseudobond, 314 residues, 2 models selected
> hide sel cartoons
> select #3/B
2438 atoms, 2476 bonds, 1 pseudobond, 314 residues, 2 models selected
> hide sel cartoons
> select #3/M
55 atoms, 58 bonds, 7 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #3/E,P
2493 atoms, 2534 bonds, 1 pseudobond, 321 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select #3/D:85,89
22 atoms, 22 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 22 atom styles
> size #3/D stickRadius 2
Changed 2476 bond radii
> style sel stick
Changed 22 atom styles
> style sel stick
Changed 22 atom styles
> style sel stick
Changed 22 atom styles
> size #3/D stickRadius 0.5
Changed 2476 bond radii
> select add #3
15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 3 models selected
> select subtract #3
2 models selected
> select #3/A
2438 atoms, 2476 bonds, 1 pseudobond, 314 residues, 2 models selected
> show sel cartoons
[Repeated 1 time(s)]
> hide sel cartoons
> select #3/B
2438 atoms, 2476 bonds, 1 pseudobond, 314 residues, 2 models selected
> show sel cartoons
> select add #3
15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 2 models selected
> select subtract #3
2 models selected
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
> RAD54/BRCA2struct1.tif" width 884 height 589 supersample 3
> select #3/C,D
4876 atoms, 4952 bonds, 2 pseudobonds, 628 residues, 2 models selected
> coulombic sel
Coulombic values for J216_011_volume_map_ABCEF.pdb_C SES surface #3.2:
minimum, -26.80, mean -0.75, maximum 13.88
Coulombic values for J216_011_volume_map_ABCEF.pdb_D SES surface #3.3:
minimum, -27.43, mean -0.73, maximum 14.12
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic sel
Coulombic values for J216_011_volume_map_ABCEF.pdb_C SES surface #3.2:
minimum, -26.80, mean -0.75, maximum 13.88
Coulombic values for J216_011_volume_map_ABCEF.pdb_D SES surface #3.3:
minimum, -27.43, mean -0.73, maximum 14.12
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
[Repeated 2 time(s)]
> show sel surfaces
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right zoom
> transparency sel 50
> transparency sel 0
> select #3/C:175
8 atoms, 7 bonds, 1 residue, 1 model selected
> transparency sel 50
> show sel atoms
[Repeated 2 time(s)]
> style sel stick
Changed 8 atom styles
> hide sel surfaces
> select #3/C
2438 atoms, 2476 bonds, 1 pseudobond, 314 residues, 2 models selected
> hide sel surfaces
[Repeated 2 time(s)]
> show sel surfaces
> select #3/C:213
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel surfaces
> style sel stick
Changed 9 atom styles
> select #3/C
2438 atoms, 2476 bonds, 1 pseudobond, 314 residues, 2 models selected
> hide sel surfaces
> select #3/C
2438 atoms, 2476 bonds, 1 pseudobond, 314 residues, 2 models selected
> select #3/B,D
4876 atoms, 4952 bonds, 2 pseudobonds, 628 residues, 2 models selected
> show sel surfaces
> select #3/B,D
4876 atoms, 4952 bonds, 2 pseudobonds, 628 residues, 2 models selected
> color sel wheat
> select add #3
15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 4 models selected
> select subtract #3
3 models selected
> hide atoms
> select #3/O
55 atoms, 58 bonds, 7 residues, 1 model selected
> show sel atoms
> select add #3
15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 2 models selected
> select subtract #3
3 models selected
> ui mousemode right translate
> ui mousemode right zoom
> select #3/O,P,M,N
220 atoms, 232 bonds, 28 residues, 1 model selected
> show sel cartoons
[Repeated 2 time(s)]
> select add #3
15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 2 models selected
> select subtract #3
3 models selected
> ui mousemode right translate
> select #3/F
2438 atoms, 2476 bonds, 1 pseudobond, 314 residues, 2 models selected
> hide sel cartoons
> select #3/D:85,89
22 atoms, 22 bonds, 2 residues, 1 model selected
> color sel green
> select add #3
15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 3 models selected
> select subtract #3
3 models selected
> color sel orange
> select #3/D:85,89
22 atoms, 22 bonds, 2 residues, 1 model selected
> color sel orange
> select add #3
15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 3 models selected
> select subtract #3
3 models selected
> select #3/X
360 atoms, 395 bonds, 18 residues, 1 model selected
> hide sel cartoons
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
> RAD54/BRCA2mono.tif" width 670 height 583 supersample 3
> select #3/C:179,180,183
20 atoms, 18 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 20 atom styles
> ui mousemode right zoom
> show #!1 models
> select add #3
15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 3 models selected
> select subtract #3
3 models selected
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!1 models
> open /Users/sz140275local/Downloads/newPDBfit-
> coot-10_real_space_refined_002.pdb
Chain information for newPDBfit-coot-10_real_space_refined_002.pdb #4
---
Chain | Description
A B C D E F | No description available
M N O P Q R | No description available
X | No description available
> hide #!3 models
> hide #!1 models
> open /Users/sz140275local/Downloads/cryosparc_P26_J362_012_volume_map.mrc
Opened cryosparc_P26_J362_012_volume_map.mrc as #5, grid size 336,336,336,
pixel 0.73, shown at level 0.0236, step 2, values float32
> open
> /Users/sz140275local/Downloads/cryosparc_P26_J362_012_volume_map_sharp.mrc
Opened cryosparc_P26_J362_012_volume_map_sharp.mrc as #6, grid size
336,336,336, pixel 0.73, shown at level 0.0403, step 2, values float32
> hide #!4 models
> hide #!5 models
> surface dust #6 size 7.3
> show #!4 models
> hide #!4 atoms
> show #!4 cartoons
> transparency #6.1 50
> select #6/O,P,M,N
Nothing selected
> color sel red
> select #6/R,P,Q,
Expected an objects specifier or a keyword
> select #6/R,P,Q,M,N,O
Nothing selected
> select #4/R,P,Q,M,N,O
408 atoms, 426 bonds, 48 residues, 1 model selected
> color sel red
> select add #4
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 2 models selected
> select subtract #4
Nothing selected
> ui mousemode right translate
> color zone #6 near #4 distance 4.38
> transparency #6.1 0
> transparency #6.1 50
> hide #!6 models
> select #4/R,P,Q,M,N,O
408 atoms, 426 bonds, 48 residues, 1 model selected
> show sel atoms
> select add #4
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 2 models selected
> select subtract #4
Nothing selected
> show #!6 models
> ui mousemode right zoom
> volume #6 level 0.0257
> color zone #6 near #4 distance 4.38
> transparency #6.1 0
> transparency #6.1 50
> ui mousemode right translate
> volume #6 level 0.04401
> color zone #6 near #4 distance 4.38
> transparency #6.1 0
> transparency #6.1 50
> volume #6 level 0.03485
> color zone #6 near #4 distance 4.38
> transparency #6.1 0
> transparency #6.1 50
> hide #!4 models
> show #!5 models
> hide #!6 models
> show #!4 models
> color zone #5 near #4 distance 4.38
> transparency #5.1 50
> ui mousemode right zoom
> select #4/ATP*
Nothing selected
> hide #!5 models
> select #4/ATP
Nothing selected
> select #4/A:ATP*
31 atoms, 33 bonds, 1 residue, 1 model selected
> show sel atoms
> select #4/B,C,D:ATP*
93 atoms, 99 bonds, 3 residues, 1 model selected
> show sel atoms
> select #4/A,B,C,D:Mg*
8 atoms, 8 residues, 1 model selected
> show sel atoms
> select add #4
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 2 models selected
> select subtract #4
Nothing selected
> show #!5 models
> volume #6 level 0.04767
> hide #!6 models
> volume #5 level 0.0359
> color zone #5 near #4 distance 4.38
> transparency #5.1 50
> ui mousemode right translate
> ui mousemode right zoom
> select #4/X
360 atoms, 395 bonds, 18 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 360 atom styles
> select add #4
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 2 models selected
> select subtract #4
Nothing selected
> close #2-3
> close #1
> open "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
> structure RAD54B 07072025/cryosparc_P26_J402_011_volume_map.mrc"
Opened cryosparc_P26_J402_011_volume_map.mrc as #1, grid size 336,336,336,
pixel 0.745, shown at level 0.0227, step 2, values float32
> open "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
> structure RAD54B 07072025/cryosparc_P26_J402_011_volume_map_sharp.mrc"
Opened cryosparc_P26_J402_011_volume_map_sharp.mrc as #2, grid size
336,336,336, pixel 0.745, shown at level 0.0343, step 2, values float32
> hide #!4 models
> hide #!2 models
> hide #!1 models
> show #!6 models
> hide #!6 models
> open "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
> structure RAD54B 07072025/newPDBfit-coot-10_real_space_refined_002.pdb"
Chain information for newPDBfit-coot-10_real_space_refined_002.pdb #3
---
Chain | Description
A B C D E F | No description available
M N O P Q R | No description available
X | No description available
> hide #!5 models
> close #4
> hide atoms
> show cartoons
> hide #!3 models
> show #!5 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!5 models
> show #!6 models
> color #6 #95d3fa80 models
> color #6 #decffa80 models
> color #6 #fac9bb80 models
> show #!3 models
> hide cartoons
> select #3/X
360 atoms, 395 bonds, 18 residues, 1 model selected
> show sel cartoons
> color sel lime
> select #3/A=ATP*
Expected an objects specifier or a keyword
> select #3/A:ATP*
31 atoms, 33 bonds, 1 residue, 1 model selected
> select #3/A,B,C,D,E,F:ATP*
124 atoms, 132 bonds, 4 residues, 1 model selected
> select #3/A,B,C,D,E,F,G:ATP*
124 atoms, 132 bonds, 4 residues, 1 model selected
> style sel stick
Changed 124 atom styles
> style sel stick
Changed 124 atom styles
> show sel atoms
> color sel blue
> select #3/M,N,O,P,Q,R,S,T
408 atoms, 426 bonds, 48 residues, 1 model selected
> show sel cartoons
> show sel atoms
> select #3/M,N,O,P,Q,R,S,T
408 atoms, 426 bonds, 48 residues, 1 model selected
> color sel red
> select #3/X
360 atoms, 395 bonds, 18 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 360 atom styles
> select add #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 2 models selected
> select subtract #3
Nothing selected
> volume #6 level 0.03485
> color zone #6 near #3 distance 4.38
> transparency #6.1 0
> transparency #6.1 50
> ui mousemode right translate
> volume #6 level 0.03
> volume #6 level 0.02
> volume #6 level 0.04
> color zone #6 near #3 distance 4.38
> transparency #6.1 0
> transparency #6.1 50
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
> RAD54/BRCA2filaments.tif" width 769 height 709 supersample 3
> select #3/M,N,O,P,Q,R,S,T:10
54 atoms, 48 bonds, 6 residues, 1 model selected
> hide sel atoms
> select add #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 2 models selected
> select subtract #3
Nothing selected
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
> RAD54/BRCA2filaments.tif" width 769 height 709 supersample 3
[Repeated 1 time(s)]
> hide #!3 models
> show #!3 models
> hide #!6 models
> select #3/D
2471 atoms, 2509 bonds, 1 pseudobond, 317 residues, 2 models selected
> show sel cartoons
[Repeated 1 time(s)]
> hide sel cartoons
> select #3/E
2438 atoms, 2476 bonds, 1 pseudobond, 314 residues, 2 models selected
> show sel cartoons
[Repeated 1 time(s)]
> hide sel cartoons
> select #3/C
2471 atoms, 2509 bonds, 1 pseudobond, 317 residues, 2 models selected
> show sel cartoons
> select #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 2 models selected
> show sel surfaces
> select #3/C
2471 atoms, 2509 bonds, 1 pseudobond, 317 residues, 2 models selected
> hide sel surfaces
> select #3/O
68 atoms, 71 bonds, 8 residues, 1 model selected
> hide sel surfaces
> select add #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected
> select subtract #3
13 models selected
> select #3/X
360 atoms, 395 bonds, 18 residues, 1 model selected
> hide sel surfaces
> select add #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected
> select subtract #3
13 models selected
> cartoon style coil width 2 thickness 1.5
> cartoon style coil width 1.5 thickness 1.5
> cartoon style coil width 1.5 thickness 1
> cartoon style helix width 1.5 thickness 1
> cartoon style strand width 1.5 thickness 1
> cartoon style coil width 1 thickness 1
> cartoon style coil width 1 thickness 0.8
> size #3/D stickRadius 0.5
Changed 2509 bond radii
> size #3/D stickRadius 1
Changed 2509 bond radii
> size #3 stickRadius 1
Changed 15810 bond radii
> size #3 stickRadius 0.4
Changed 15810 bond radii
> select #3/C
2471 atoms, 2509 bonds, 1 pseudobond, 317 residues, 2 models selected
> color sel wheat
> select add #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected
> select subtract #3
13 models selected
> select #3/D
2471 atoms, 2509 bonds, 1 pseudobond, 317 residues, 2 models selected
> color #3/D:85,89
> color #3/D:85,89 orange
> select add #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected
> select subtract #3
13 models selected
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
> RAD54/BRCA2filaments2.tif" width 769 height 709 supersample 3
> show #!6 models
> volume #2 level 0.02615
> hide #!2 models
> hide #!6 models
> show #!6 models
> volume #2 level 0.01936
> hide #!6 models
> show #!6 models
> hide #!2 models
> volume #6 level 0.03451
> color zone #6 near #3 distance 4.38
> transparency #3.2-14#6.1 0
> transparency #3.2-14#6.1 50
> volume #6 level 0.02169
> color zone #6 near #3 distance 4.38
> transparency #3.2-14#6.1 0
> transparency #3.2-14#6.1 50
> volume #6 level 0.03267
> color zone #6 near #3 distance 4.38
> transparency #3.2-14#6.1 0
> transparency #3.2-14#6.1 50
> hide #!6 models
> show #!5 models
> volume #5 level 0.0125
> color zone #5 near #3 distance 4.38
> transparency #3.2-14#5.1 0
> transparency #3.2-14#5.1 50
> hide #!5 models
> select /O:10
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select add #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected
> select subtract #3
13 models selected
> show #!5 models
> volume #5 level 0.01455
> color zone #5 near #3 distance 4.38
> transparency #3.2-14#5.1 0
> transparency #3.2-14#5.1 50
> hide #!5 models
> show #!6 models
> volume #6 level 0.04
> color zone #6 near #3 distance 4.38
> transparency #3.2-14#6.1 0
> transparency #3.2-14#6.1 50
> color #3/O:3,10
> show atoms
[Repeated 1 time(s)]
> hide atoms
> color #3/O
> hide #!6 models
> color #3/O
> show atoms
> hide atoms
> select add #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 2 models selected
> color #3/O
> select #3/O
68 atoms, 71 bonds, 8 residues, 1 model selected
> show sel atoms
> select #3/O:3,10
18 atoms, 16 bonds, 2 residues, 1 model selected
> hide sel atoms
> select add #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected
> select subtract #3
13 models selected
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
> RAD54/BRCA2filaments2.tif" width 769 height 709 supersample 3
> select #3/O:C
Nothing selected
> hide cartoons
> show surfaces
> hide surfaces
> select #3/
Expected an objects specifier or a keyword
> hide surfaces
> show cartoons
> hide #!3 models
> show #!6 models
> select #3/M,N,O,P,Q,R,S,T
408 atoms, 426 bonds, 48 residues, 1 model selected
> select #3/M,N,O,P,Q,R,S,T
408 atoms, 426 bonds, 48 residues, 1 model selected
> transparency #6.1 0
> transparency #6.1 50
> show #!3 models
> select #3/
Expected an objects specifier or a keyword
> hide sel cartoons
> hide sel atoms
> hide sel surfaces
> hide sel cartoons
> select #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 2 models selected
> hide sel cartoons
> select #3/M,N,O,P,Q,R,S,T
408 atoms, 426 bonds, 48 residues, 1 model selected
> show sel cartoons
> show sel atoms
> select #3/M,N,O,P,Q,R,S,T:3,10
108 atoms, 96 bonds, 12 residues, 1 model selected
> hide sel atoms
> select #3/X
360 atoms, 395 bonds, 18 residues, 1 model selected
> hide sel atoms
> show sel atoms
> select #3/A,B,C,D,E,F,G:ATP*
124 atoms, 132 bonds, 4 residues, 1 model selected
> show sel atoms
> select add #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 2 models selected
> select subtract #3
13 models selected
> hide #!6 models
> select #3/A,B,C,D,E,F,G:ATP*
124 atoms, 132 bonds, 4 residues, 1 model selected
> color sel blue
> select add #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 2 models selected
> select subtract #3
13 models selected
> show #!6 models
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
> RAD54/BRCA2filaments.tif" width 769 height 709 supersample 3
> color #3/C
> hide surfaces
[Repeated 1 time(s)]
> select #3/C
2471 atoms, 2509 bonds, 1 pseudobond, 317 residues, 2 models selected
> hide sel surfaces
> show sel cartoons
> hide sel surfaces
> select add #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected
> select subtract #3
13 models selected
> hide #!6 models
> show surfaces
> select #3/D:85,89
22 atoms, 22 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 22 atom styles
> select add #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected
> select subtract #3
13 models selected
> select #3/M,N,O,P,Q,R,S,T
408 atoms, 426 bonds, 48 residues, 1 model selected
> hide sel surfaces
> select add #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 8 models selected
> select subtract #3
13 models selected
> select #3/Z
Nothing selected
> hide surfaces
> show surfaces
> select #3/X
360 atoms, 395 bonds, 18 residues, 1 model selected
> hide sel surfaces
> select #3/M,N,O,P,Q,R,S,T
408 atoms, 426 bonds, 48 residues, 1 model selected
> hide sel surfaces
> select add #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 8 models selected
> select subtract #3
13 models selected
> select #3/C
2471 atoms, 2509 bonds, 1 pseudobond, 317 residues, 2 models selected
> hide sel surfaces
> select add #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected
> select subtract #3
13 models selected
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
> RAD54/BRCA2filaments2.tif" width 769 height 709 supersample 3
> select #3/
Expected an objects specifier or a keyword
> transparency #3.2-14 0
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
> RAD54/BRCA2filaments2.tif" width 769 height 709 supersample 3
> open /Users/sz140275local/Downloads/RAD54-J402_m1_real_space_refined_001.pdb
Chain information for RAD54-J402_m1_real_space_refined_001.pdb #4
---
Chain | Description
A B C D E F | No description available
M N O P Q R | No description available
X | No description available
> hide #!4 models
> hide #!3 models
> show #!4 models
> hide #!4 cartoons
> hide #!4 atoms
> show #!4 cartoons
> ui tool show "Show Sequence Viewer"
> sequence chain #4/O
Alignment identifier is 4/O
> hide #!4 models
> show #!3 models
> select #3/C:85,89
22 atoms, 22 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 22 atom styles
> select add #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected
> select subtract #3
13 models selected
> select #3/C:85,89
22 atoms, 22 bonds, 2 residues, 1 model selected
> color sel orange
> select add #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected
> select subtract #3
13 models selected
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
> RAD54/BRCA2filaments2.tif" width 560 height 701 supersample 3
> open 7C9C
7c9c title:
Human DMC1 pre-synaptic complexes [more info...]
Chain information for 7c9c #7
---
Chain | Description | UniProt
A B C | Meiotic recombination protein DMC1/LIM15 homolog | DMC1_HUMAN 1-340
D | DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*T)-3') |
Non-standard residues in 7c9c #7
---
ANP — phosphoaminophosphonic acid-adenylate ester
CA — calcium ion
> mmaker #7 to #3
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker newPDBfit-coot-10_real_space_refined_002.pdb, chain E (#3) with
7c9c, chain B (#7), sequence alignment score = 1478.4
RMSD between 302 pruned atom pairs is 0.679 angstroms; (across all 308 pairs:
0.775)
> select #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 2 models selected
> hide sel surfaces
> show sel cartoons
> select subtract #3
13 models selected
> select #3/A,B,C
7413 atoms, 7528 bonds, 3 pseudobonds, 951 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select #3/M,N,O
204 atoms, 213 bonds, 24 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> ~label (#!3 & sel) residues
> ~label (#!3 & sel) atoms
> hide #!7 models
> show #!7 models
> select #7
7452 atoms, 7586 bonds, 10 pseudobonds, 939 residues, 4 models selected
> ~label (#!7 & sel) residues
> ~label (#!7 & sel) atoms
> select subtract #7
Nothing selected
> select #3/C,D,E,F,G:85,89
88 atoms, 88 bonds, 8 residues, 1 model selected
> hide sel atoms
> color sel palegreen blue
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel light blue
> select add #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 6 models selected
> select subtract #3
13 models selected
> select #7
7452 atoms, 7586 bonds, 10 pseudobonds, 939 residues, 4 models selected
> ui tool show "Selection Inspector"
> delete label
Missing or invalid "atoms" argument: invalid atoms specifier
> delete
Missing or invalid "atoms" argument: empty atom specifier
> delete #7/B:276-282
> select #7/B:275-283
4 atoms, 3 bonds, 1 residue, 1 model selected
> ~label sel residues
> ~label sel atoms
> select add #7
7452 atoms, 7586 bonds, 10 pseudobonds, 939 residues, 4 models selected
> select subtract #7
Nothing selected
> select #3/M,N,O,P,Q,R,S,T
408 atoms, 426 bonds, 48 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> select #3/D:132
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> select #3/D:162
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> select #3/D:133
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> select #7
7452 atoms, 7586 bonds, 10 pseudobonds, 939 residues, 4 models selected
> hide sel atoms
> show sel atoms
> hide sel atoms
> show sel atoms
> hide sel atoms
> select #7/D
180 atoms, 197 bonds, 9 residues, 1 model selected
> show sel atoms
> select #7/A,B,C:ANP*
93 atoms, 99 bonds, 3 residues, 1 model selected
> show sel atoms
> select add #7
7452 atoms, 7586 bonds, 10 pseudobonds, 939 residues, 4 models selected
> select subtract #7
Nothing selected
> select #7/A,B,C:
Expected an objects specifier or a keyword
> select #7/A,B,C
7272 atoms, 7389 bonds, 10 pseudobonds, 930 residues, 3 models selected
> label delete
> select add #7
7452 atoms, 7586 bonds, 10 pseudobonds, 939 residues, 3 models selected
> select subtract #7
Nothing selected
> select #7/D
180 atoms, 197 bonds, 9 residues, 1 model selected
> show sel cartoons
> select add #7
7452 atoms, 7586 bonds, 10 pseudobonds, 939 residues, 3 models selected
> select subtract #7
Nothing selected
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
> RAD54/BRCA2compC9C7.tif" width 890 height 709 supersample 3
> select #7/P
Nothing selected
> show #!3,7 cartoons
> hide #!3,7 cartoons
> show #!3,7 cartoons
> hide #!3,7 cartoons
> hide #!3 models
> show #!3 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> select #7
7452 atoms, 7586 bonds, 10 pseudobonds, 939 residues, 3 models selected
> show sel cartoons
> select #3/A,B,C
7413 atoms, 7528 bonds, 3 pseudobonds, 951 residues, 2 models selected
> show sel cartoons
[Repeated 1 time(s)]
> hide sel cartoons
> select #3/D,E,F
7347 atoms, 7461 bonds, 3 pseudobonds, 945 residues, 2 models selected
> show sel cartoons
> select add #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 5 models selected
> select subtract #3
13 models selected
> select #3/O,P
136 atoms, 142 bonds, 16 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #3/P
68 atoms, 71 bonds, 8 residues, 1 model selected
> show sel cartoons
> select add #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected
> select subtract #3
13 models selected
> mmaker #7/A to #3/D
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker newPDBfit-coot-10_real_space_refined_002.pdb, chain D (#3) with
7c9c, chain A (#7), sequence alignment score = 1458.6
RMSD between 301 pruned atom pairs is 0.668 angstroms; (across all 308 pairs:
0.819)
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
> RAD54/BRCA2compC9C7.zoomtif.tif" width 890 height 709 supersample 3
> select #3/P
68 atoms, 71 bonds, 8 residues, 1 model selected
> hide sel cartoons
> select #3/D:ATP*
31 atoms, 33 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/X
360 atoms, 395 bonds, 18 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #7/D
180 atoms, 197 bonds, 9 residues, 1 model selected
> color sel black
> select add #7
7452 atoms, 7586 bonds, 10 pseudobonds, 939 residues, 3 models selected
> select subtract #7
Nothing selected
> select #7/*ATP*
Nothing selected
> select #7/*ANP*
Nothing selected
> select #7/A,B,C,D:ANP*
93 atoms, 99 bonds, 3 residues, 1 model selected
> color sel black
> select add #7
7452 atoms, 7586 bonds, 10 pseudobonds, 939 residues, 3 models selected
> select subtract #7
Nothing selected
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
> RAD54/BRCA2compC9C7.tif" width 890 height 709 supersample 3
> mmaker #7/A,B,C to #3/D,E,F
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker newPDBfit-coot-10_real_space_refined_002.pdb, chain E (#3) with
7c9c, chain B (#7), sequence alignment score = 1478.4
RMSD between 302 pruned atom pairs is 0.679 angstroms; (across all 308 pairs:
0.775)
> mmaker #7/A,B,C to #3/D,E,F
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker newPDBfit-coot-10_real_space_refined_002.pdb, chain E (#3) with
7c9c, chain B (#7), sequence alignment score = 1478.4
RMSD between 302 pruned atom pairs is 0.679 angstroms; (across all 308 pairs:
0.775)
> mmaker #7/A,B,C to #3/D,E,F
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker newPDBfit-coot-10_real_space_refined_002.pdb, chain E (#3) with
7c9c, chain B (#7), sequence alignment score = 1478.4
RMSD between 302 pruned atom pairs is 0.679 angstroms; (across all 308 pairs:
0.775)
> mmaker #7/A,B,C to #3/D,E,F
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker newPDBfit-coot-10_real_space_refined_002.pdb, chain E (#3) with
7c9c, chain B (#7), sequence alignment score = 1478.4
RMSD between 302 pruned atom pairs is 0.679 angstroms; (across all 308 pairs:
0.775)
> mmaker #7/A,B,C to #3/D,E,F
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker newPDBfit-coot-10_real_space_refined_002.pdb, chain E (#3) with
7c9c, chain B (#7), sequence alignment score = 1478.4
RMSD between 302 pruned atom pairs is 0.679 angstroms; (across all 308 pairs:
0.775)
> mmaker #7/A to #3/D
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker newPDBfit-coot-10_real_space_refined_002.pdb, chain D (#3) with
7c9c, chain A (#7), sequence alignment score = 1458.6
RMSD between 301 pruned atom pairs is 0.668 angstroms; (across all 308 pairs:
0.819)
> mmaker #7/A,B,C to #3/D,E,F
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker newPDBfit-coot-10_real_space_refined_002.pdb, chain E (#3) with
7c9c, chain B (#7), sequence alignment score = 1478.4
RMSD between 302 pruned atom pairs is 0.679 angstroms; (across all 308 pairs:
0.775)
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
> RAD54/BRCA2compC9C7.tif" width 890 height 709 supersample 3
> hide #!7 models
> hide #!3 models
> show #!6 models
> show #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> hide #!6 models
> show #!7 models
> hide #!4 models
> show #!3 models
> select #3/E:ATP*
Nothing selected
> show #!3,7 atoms
> hide #!3,7 atoms
> select #3/*:ATP*
124 atoms, 132 bonds, 4 residues, 1 model selected
> show sel atoms
> hide sel atoms
> select #3/D:ATP*
31 atoms, 33 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7/*:ATP*
Nothing selected
> select #7/*:ANP*
93 atoms, 99 bonds, 3 residues, 1 model selected
> show sel atoms
> select add #7
7452 atoms, 7586 bonds, 10 pseudobonds, 939 residues, 3 models selected
> select subtract #7
Nothing selected
> select #3/O*
68 atoms, 71 bonds, 8 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #3/M*
68 atoms, 71 bonds, 8 residues, 1 model selected
> show sel atoms
> hide sel atoms
> select #3/R*
68 atoms, 71 bonds, 8 residues, 1 model selected
> show sel atoms
> hide sel atoms
> select #3/Q*
68 atoms, 71 bonds, 8 residues, 1 model selected
> show sel atoms
> hide sel atoms
> hide sel cartoons
> hide sel atoms
> select #3/P*
68 atoms, 71 bonds, 8 residues, 1 model selected
> show sel atoms
> select #3/P,Q*
136 atoms, 142 bonds, 16 residues, 1 model selected
> show sel atoms
> select add #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 4 models selected
> select subtract #3
13 models selected
> select #3/X
360 atoms, 395 bonds, 18 residues, 1 model selected
> show sel atoms
> select add #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected
> hide #!3 models
> show #!3 models
> select subtract #3
13 models selected
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
> RAD54/BRCA2compC9C7.zoomtif.tif" width 890 height 709 supersample 3
> select #3/P,Q:3,10
36 atoms, 32 bonds, 4 residues, 1 model selected
> hide sel atoms
> select #3/P,Q
136 atoms, 142 bonds, 16 residues, 1 model selected
> show sel cartoons
> select add #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 4 models selected
> select subtract #3
13 models selected
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
> RAD54/BRCA2compC9C7.zoomtif.tif" width 875 height 694 supersample 3
> hide #!7 models
> select add #7
7452 atoms, 7586 bonds, 10 pseudobonds, 939 residues, 3 models selected
> select subtract #7
Nothing selected
> select #3/F:ATP*
Nothing selected
> show #!3 atoms
> hide #!3 atoms
> select #3/E:ATP*
Nothing selected
> hide #!3 atoms
[Repeated 1 time(s)]
> show #!3 atoms
> hide #!3 atoms
> select #3/E:ATP*
Nothing selected
> show #!3 atoms
> hide #!3 atoms
> select #3/E
2438 atoms, 2476 bonds, 1 pseudobond, 314 residues, 2 models selected
> show sel atoms
> hide sel atoms
> select #3/E:ATP*
Nothing selected
> show #!3 atoms
> hide #!3 atoms
> select #3/E:ATP*
Nothing selected
> select #3/D:ATP*
31 atoms, 33 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/B,D:ATP*
62 atoms, 66 bonds, 2 residues, 1 model selected
> show sel atoms
> select #3/C,D:ATP*
62 atoms, 66 bonds, 2 residues, 1 model selected
> show sel atoms
> select #3/Q
68 atoms, 71 bonds, 8 residues, 1 model selected
> hide sel cartoons
> select #3/E
2438 atoms, 2476 bonds, 1 pseudobond, 314 residues, 2 models selected
> hide sel cartoons
> show sel cartoons
> select #3/F
2438 atoms, 2476 bonds, 1 pseudobond, 314 residues, 2 models selected
> hide sel cartoons
> select #3/F
2438 atoms, 2476 bonds, 1 pseudobond, 314 residues, 2 models selected
> select #3/P
68 atoms, 71 bonds, 8 residues, 1 model selected
> select #3/Q
68 atoms, 71 bonds, 8 residues, 1 model selected
> show sel cartoons
> select #3/B,C
4942 atoms, 5018 bonds, 2 pseudobonds, 634 residues, 2 models selected
> show sel cartoons
> select #3/O,N
136 atoms, 142 bonds, 16 residues, 1 model selected
> show sel cartoons
> select #3/M,A
2539 atoms, 2581 bonds, 1 pseudobond, 325 residues, 2 models selected
> show sel cartoons
> select #3/A:ATP*
31 atoms, 33 bonds, 1 residue, 1 model selected
> show sel cartoons
> show sel atoms
> select add #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 2 models selected
> select subtract #3
13 models selected
> show #!6 models
> hide #!6 models
> show #!6 models
> select #3/X
360 atoms, 395 bonds, 18 residues, 1 model selected
> show sel atoms
> select add #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected
> select subtract #3
13 models selected
> hide #!6 models
> select #3/B:85,89
22 atoms, 22 bonds, 2 residues, 1 model selected
> hide sel atoms
> color sel light blue
> show #!6 models
> hide #!6 models
> select #3/C:85,89
22 atoms, 22 bonds, 2 residues, 1 model selected
> color sel wheat
> show #!6 models
> color zone #6 near sel & #3 distance 4.38
[Repeated 3 time(s)]
> transparency sel 50
> select add #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected
> select subtract #3
13 models selected
> color zone #6 near #3 distance 4.38
> transparency #3.2-14#6.1 0
> transparency #3.2-14#6.1 50
> color #3/A,C,F
> color #3/A,C,F wheat
> color #3/B,D royal blue
> color zone #6 near #3 distance 4.38
> color #3/A,C,E wheat
> color zone #6 near #3 distance 4.38
> color #6 #f5dec980 models
> color #3/F wheat
> color #3/F misty rose
> color zone #6 near #3 distance 4.38
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> color #3/R misty rose
> show #!6 models
> color zone #6 near #3 distance 4.38
> color #3/M,N,O,P,Q misty rose
> show #!3 cartoons
> show #!3 atoms
> hide #!3 atoms
> select #3/M,N,O,P,Q
340 atoms, 355 bonds, 40 residues, 1 model selected
> select #3/M,N,O,P,Q
340 atoms, 355 bonds, 40 residues, 1 model selected
> show sel atoms
> select #3/M,N,O,P,Q:3,10
90 atoms, 80 bonds, 10 residues, 1 model selected
> hide sel atoms
> select #3/A,B,C,D,E:ATP*
124 atoms, 132 bonds, 4 residues, 1 model selected
> show sel atoms
> transparency #3.2-14#6.1 0
> transparency #3.2-14#6.1 50
> select #3/A,B,C,D,E:ATP*
124 atoms, 132 bonds, 4 residues, 1 model selected
> color sel black
> select #3/M,N,O,P,Q
340 atoms, 355 bonds, 40 residues, 1 model selected
> color sel red
> select add #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 7 models selected
> select subtract #3
13 models selected
> select #3/X
360 atoms, 395 bonds, 18 residues, 1 model selected
> show sel atoms
> select add #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected
> select subtract #3
13 models selected
> surface dust #6 size 7.3
[Repeated 3 time(s)]
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
> RAD54/BRCA2struct1.tif" width 890 height 709 supersample 3
> surface dust #6 size 7.3
[Repeated 1 time(s)]
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> ui mousemode right zoom
> ui mousemode right translate
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
> RAD54/BRCA2struct1.tif" width 890 height 709 supersample 3
> select #3/A,M
2539 atoms, 2581 bonds, 1 pseudobond, 325 residues, 2 models selected
> hide sel cartoons
> color #3/A,M mistyrose pink
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> hide sel cartoons
> hide sel atoms
> hide #!6 models
> color #3/F dodger blue
> color #3/F royal blue
> select #3/R
68 atoms, 71 bonds, 8 residues, 1 model selected
> show sel atoms
> select #3/R:3,10
18 atoms, 16 bonds, 2 residues, 1 model selected
> hide sel atoms
> color #3/R red
> show #!6 models
> color #6 #f4e7ce80 models
> color zone #6 near sel & #3 distance 4.38
[Repeated 1 time(s)]
> select add #6
18 atoms, 16 bonds, 2 residues, 4 models selected
> select add #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 5 models selected
> select subtract #3
15 models selected
> color zone #6 near #3 distance 4.38
> select subtract #6
Nothing selected
> select add #6
2 models selected
> select subtract #6
Nothing selected
> hide #!3 models
> show #!3 models
> color #6 #f4f5d380 models
> color #3/A,M misty rose
> color zone #6 near #3 distance 4.38
> color #3/A,M white
> color zone #6 near #3 distance 4.38
> color #3/A,M lemon chiffon
> color zone #6 near #3 distance 4.38
> color #3/A,M light yellow
> color zone #6 near #3 distance 4.38
> hide #!3 models
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
> RAD54/BRCA2struct0.tif" width 890 height 709 supersample 3
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
> RAD54/BRCA2struct0b.tif" width 890 height 709 supersample 3
> ui mousemode right zoom
> ui mousemode right translate
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
> RAD54/BRCA2struct0b.tif" width 890 height 709 supersample 3
[Repeated 1 time(s)]
> show #!3 models
> transparency #3.2-14#6.1 0
> transparency #3.2-14#6.1 50
> select #3/D
2471 atoms, 2509 bonds, 1 pseudobond, 317 residues, 2 models selected
> transparency sel 0
> transparency sel 50
> select add #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected
> select subtract #3
13 models selected
> hide #!6 models
> select #3/X
360 atoms, 395 bonds, 18 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> select #3/E:85,89
22 atoms, 22 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 22 atom styles
> color sel orange
> select add #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected
> select subtract #3
13 models selected
> show #!6 models
> volume #6 level 0.02869
> color zone #6 near #3 distance 4.38
> transparency #3.2-14#6.1 0
> transparency #3.2-14#6.1 50
> volume #6 level 0.05131
> volume #6 level 0.03
> color zone #6 near #3 distance 4.38
> volume #6 level 0.035
> transparency #3.2-14#6.1 0
> transparency #3.2-14#6.1 50
> hide #!6 models
> show #!6 models
> select #3/F
2438 atoms, 2476 bonds, 1 pseudobond, 314 residues, 2 models selected
> hide sel cartoons
> hide #!6 models
> show #!6 models
> select #3/D:85,89
22 atoms, 22 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel orange
> hide #!6 models
> show #!6 models
> color zone #6 near sel & #3 distance 4.38
[Repeated 1 time(s)]
> select add #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected
> select subtract #3
13 models selected
> select add #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 2 models selected
> color zone #6 near sel & #3 distance 4.38
> transparency sel 0
> transparency sel 50
> select subtract #3
13 models selected
> transparency #3.2-14#6.1 0
> transparency #3.2-14#6.1 50
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
> RAD54/BRCA2struct0c.tif" width 890 height 709 supersample 3
> hide #!6 models
> show #!6 models
> hide #!6 models
> select #3/C,E
4909 atoms, 4985 bonds, 2 pseudobonds, 631 residues, 2 models selected
> show sel surfaces
> select add #3.1
4909 atoms, 4985 bonds, 6 pseudobonds, 631 residues, 4 models selected
> select subtract #3.1
4909 atoms, 4985 bonds, 631 residues, 3 models selected
> select add #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 4 models selected
> select subtract #3
13 models selected
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
> RAD54/BRCA2struct0d.tif" width 890 height 709 supersample 3
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
> RAD54/BRCA2-07072025.cxs"
——— End of log from Mon Jul 7 15:58:39 2025 ———
opened ChimeraX session
> show #!7 models
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!6 models
> select #3/P:3,10
18 atoms, 16 bonds, 2 residues, 1 model selected
> show sel atoms
> volume #6 level 0.02208
> color zone #6 near sel & #3 distance 4.38
> select add #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected
> select subtract #3
13 models selected
> color zone #6 near #3 distance 4.38
[Repeated 1 time(s)]
> transparency #3.2-14#6.1 0
> transparency #3.2-14#6.1 50
> volume #6 level 0.02854
> color zone #6 near #3 distance 4.38
> transparency #3.2-14#6.1 0
> transparency #3.2-14#6.1 50
> volume #6 level 0.03
> color zone #6 near #3 distance 4.38
> transparency #3.2-14#6.1 0
> transparency #3.2-14#6.1 50
> volume #6 level 0.035
> color zone #6 near #3 distance 4.38
> transparency #3.2-14#6.1 0
> transparency #3.2-14#6.1 50
> hide #!6 models
> color bfactor #3/B
2471 atoms, 317 residues, 1 surfaces, atom bfactor range 59.1 to 203
> color bfactor #3/BD
No atoms specified
> color bfactor #3/D
2471 atoms, 317 residues, 1 surfaces, atom bfactor range 52.2 to 170
> color bfactor #3/B
2471 atoms, 317 residues, 1 surfaces, atom bfactor range 59.1 to 203
> hide #!3 cartoons
> show #!3 cartoons
> color #3/B royal blue
> color bfactor #3/P
68 atoms, 8 residues, 1 surfaces, atom bfactor range 104 to 145
> color #3/O wheat
> color #3/B wheat
> color #3/F wheat
> hide #!3 models
> show #!2 models
> volume #2 level 0.04171
Color zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 1 maps.
> surface dust #2 size 7.45
> show #!4 models
> ui tool show "Map Statistics"
> measure mapstats #!2
Map cryosparc_P26_J402_011_volume_map_sharp.mrc #2, step 2, minimum -0.2938,
maximum 0.57, mean 0.0008808, SD 0.01263, RMS 0.01266
> ui tool show "Map Coordinates"
> ui tool show "Fit in Map"
> fitmap #4 inMap #2
Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#4) to map
cryosparc_P26_J402_011_volume_map_sharp.mrc (#2) using 15528 atoms
average map value = 0.02136, steps = 72
shifted from previous position = 2.7
rotated from previous position = 2.26 degrees
atoms outside contour = 12054, contour level = 0.041713
Position of RAD54-J402_m1_real_space_refined_001.pdb (#4) relative to
cryosparc_P26_J402_011_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.99982960 -0.01832214 -0.00225362 4.55188201
0.01823221 0.99922246 -0.03495810 0.83149762
0.00289238 0.03491105 0.99938624 -5.85964538
Axis 0.88417881 -0.06512155 0.46258730
Axis point 0.00000000 184.92677295 22.01943861
Rotation angle (degrees) 2.26438918
Shift along axis 1.25993170
> select #4/A,M
2539 atoms, 2581 bonds, 1 pseudobond, 325 residues, 2 models selected
> fitmap sel inMap #2
Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#4) to map
cryosparc_P26_J402_011_volume_map_sharp.mrc (#2) using 2539 atoms
average map value = 0.02261, steps = 116
shifted from previous position = 1.45
rotated from previous position = 9.84 degrees
atoms outside contour = 1967, contour level = 0.041713
Position of RAD54-J402_m1_real_space_refined_001.pdb (#4) relative to
cryosparc_P26_J402_011_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.98424810 -0.09316819 -0.15025098 41.07304687
0.09430536 0.99554322 0.00044532 -15.27352811
0.14953986 -0.01460778 0.98864779 -19.15376273
Axis -0.04253453 -0.84709842 0.52973115
Axis point 151.35584707 0.00000000 257.79096684
Rotation angle (degrees) 10.19224918
Shift along axis 1.04481421
> fitmap sel inMap #2
Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#4) to map
cryosparc_P26_J402_011_volume_map_sharp.mrc (#2) using 2539 atoms
average map value = 0.02261, steps = 64
shifted from previous position = 0.0104
rotated from previous position = 0.0175 degrees
atoms outside contour = 1962, contour level = 0.041713
Position of RAD54-J402_m1_real_space_refined_001.pdb (#4) relative to
cryosparc_P26_J402_011_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.98430158 -0.09301129 -0.14999768 41.01143653
0.09414090 0.99555879 0.00043217 -15.25193280
0.14929131 -0.01454631 0.98868625 -19.13386900
Axis -0.04239536 -0.84711300 0.52971898
Axis point 151.41713045 0.00000000 257.86243105
Rotation angle (degrees) 10.17482829
Shift along axis 1.04584245
> select #4/A,M
2539 atoms, 2581 bonds, 1 pseudobond, 325 residues, 2 models selected
> select #4/B,N
2539 atoms, 2580 bonds, 1 pseudobond, 325 residues, 2 models selected
> select #4/C,O
2539 atoms, 2580 bonds, 1 pseudobond, 325 residues, 2 models selected
> select #4/D,P
2539 atoms, 2580 bonds, 1 pseudobond, 325 residues, 2 models selected
> select #4/E,Q
2506 atoms, 2547 bonds, 1 pseudobond, 322 residues, 2 models selected
> select #4/F,R
2506 atoms, 2547 bonds, 1 pseudobond, 322 residues, 2 models selected
> select #4/F,R
2506 atoms, 2547 bonds, 1 pseudobond, 322 residues, 2 models selected
> fitmap sel inMap #2 moveWholeMolecules false
Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#4) to map
cryosparc_P26_J402_011_volume_map_sharp.mrc (#2) using 2506 atoms
average map value = 0.01676, steps = 100
shifted from previous position = 1.8
rotated from previous position = 8.28 degrees
atoms outside contour = 2133, contour level = 0.041713
> fitmap sel inMap #2 moveWholeMolecules false
Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#4) to map
cryosparc_P26_J402_011_volume_map_sharp.mrc (#2) using 2506 atoms
average map value = 0.01676, steps = 60
shifted from previous position = 0.0175
rotated from previous position = 0.0306 degrees
atoms outside contour = 2134, contour level = 0.041713
> fitmap sel inMap #2 moveWholeMolecules false
Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#4) to map
cryosparc_P26_J402_011_volume_map_sharp.mrc (#2) using 2506 atoms
average map value = 0.01676, steps = 44
shifted from previous position = 0.0118
rotated from previous position = 0.0214 degrees
atoms outside contour = 2135, contour level = 0.041713
> fitmap sel inMap #2 moveWholeMolecules false
Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#4) to map
cryosparc_P26_J402_011_volume_map_sharp.mrc (#2) using 2506 atoms
average map value = 0.01676, steps = 64
shifted from previous position = 0.0021
rotated from previous position = 0.0043 degrees
atoms outside contour = 2133, contour level = 0.041713
> fitmap sel inMap #2 moveWholeMolecules false
Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#4) to map
cryosparc_P26_J402_011_volume_map_sharp.mrc (#2) using 2506 atoms
average map value = 0.01676, steps = 64
shifted from previous position = 0.00268
rotated from previous position = 0.0039 degrees
atoms outside contour = 2135, contour level = 0.041713
> close #2
> close #4
> open "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
> structure RAD54B 07072025/newPDBfit-coot-10_real_space_refined_002.pdb"
Chain information for newPDBfit-coot-10_real_space_refined_002.pdb #2
---
Chain | Description
A B C D E F | No description available
M N O P Q R | No description available
X | No description available
> open "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
> structure RAD54B 07072025/cryosparc_P26_J402_011_volume_map_sharp.mrc"
Opened cryosparc_P26_J402_011_volume_map_sharp.mrc as #4, grid size
336,336,336, pixel 0.745, shown at level 0.0343, step 2, values float32
> surface dust #4 size 7.45
> hide #!2 atoms
> show #!2 atoms
[Repeated 1 time(s)]
> hide #!2 atoms
> hide #!2 cartoons
> show #!2 cartoons
> hide #!2 models
> open "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
> structure RAD54B 07072025/RAD54-J402_m1_real_space_refined_001.pdb"
Chain information for RAD54-J402_m1_real_space_refined_001.pdb #5
---
Chain | Description
A B C D E F | No description available
M N O P Q R | No description available
X | No description available
> select add #5
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> select #4/A,M
Nothing selected
> select #5/A,M
2539 atoms, 2581 bonds, 1 pseudobond, 325 residues, 2 models selected
> fitmap sel inMap #4 moveWholeMolecules false
Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#5) to map
cryosparc_P26_J402_011_volume_map_sharp.mrc (#4) using 2539 atoms
average map value = 0.02263, steps = 116
shifted from previous position = 2.54
rotated from previous position = 6.47 degrees
atoms outside contour = 1924, contour level = 0.0343
> ui mousemode right "translate selected models"
> view matrix models #5,1,0,0,2.953,0,1,0,-4.242,0,0,1,-0.79188
> fitmap sel inMap #4 moveWholeMolecules false
Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#5) to map
cryosparc_P26_J402_011_volume_map_sharp.mrc (#4) using 2539 atoms
average map value = 0.0212, steps = 116
shifted from previous position = 1.4
rotated from previous position = 8.19 degrees
atoms outside contour = 1949, contour level = 0.0343
> view matrix models #5,1,0,0,1.0377,0,1,0,-0.69388,0,0,1,-1.3528
> view matrix models #5,1,0,0,-0.13682,0,1,0,-2.2411,0,0,1,-0.70572
> select #5/A,M
2539 atoms, 2581 bonds, 1 pseudobond, 325 residues, 2 models selected
> fitmap sel inMap #4 moveWholeMolecules false
Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#5) to map
cryosparc_P26_J402_011_volume_map_sharp.mrc (#4) using 2539 atoms
average map value = 0.1051, steps = 72
shifted from previous position = 2.02
rotated from previous position = 2.45 degrees
atoms outside contour = 452, contour level = 0.0343
> select #5/B,N
2539 atoms, 2580 bonds, 1 pseudobond, 325 residues, 2 models selected
> fitmap sel inMap #4 moveWholeMolecules false
Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#5) to map
cryosparc_P26_J402_011_volume_map_sharp.mrc (#4) using 2539 atoms
average map value = 0.02419, steps = 104
shifted from previous position = 1.99
rotated from previous position = 7.47 degrees
atoms outside contour = 1881, contour level = 0.0343
> view matrix models #5,1,0,0,-2.8013,0,1,0,-6.3378,0,0,1,-1.9553
> fitmap sel inMap #4 moveWholeMolecules false
Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#5) to map
cryosparc_P26_J402_011_volume_map_sharp.mrc (#4) using 2539 atoms
average map value = 0.1297, steps = 140
shifted from previous position = 4.11
rotated from previous position = 7.46 degrees
atoms outside contour = 322, contour level = 0.0343
> select #5/A,M
2539 atoms, 2581 bonds, 1 pseudobond, 325 residues, 2 models selected
> fitmap sel inMap #4 moveWholeMolecules false
Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#5) to map
cryosparc_P26_J402_011_volume_map_sharp.mrc (#4) using 2539 atoms
average map value = 0.02559, steps = 80
shifted from previous position = 0.958
rotated from previous position = 5.73 degrees
atoms outside contour = 1806, contour level = 0.0343
> select #5/A,M
2539 atoms, 2581 bonds, 1 pseudobond, 325 residues, 2 models selected
> view matrix models #5,1,0,0,-0.91106,0,1,0,-1.7616,0,0,1,-4.2822
> select #5/A,M
2539 atoms, 2581 bonds, 1 pseudobond, 325 residues, 2 models selected
> fitmap sel inMap #4 moveWholeMolecules false
Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#5) to map
cryosparc_P26_J402_011_volume_map_sharp.mrc (#4) using 2539 atoms
average map value = 0.1051, steps = 68
shifted from previous position = 2.78
rotated from previous position = 5.72 degrees
atoms outside contour = 451, contour level = 0.0343
> select #5/B,N
2539 atoms, 2580 bonds, 1 pseudobond, 325 residues, 2 models selected
> fitmap sel inMap #4 moveWholeMolecules false
Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#5) to map
cryosparc_P26_J402_011_volume_map_sharp.mrc (#4) using 2539 atoms
average map value = 0.0267, steps = 108
shifted from previous position = 1.2
rotated from previous position = 5.25 degrees
atoms outside contour = 1812, contour level = 0.0343
> fitmap sel inMap #4 moveWholeMolecules false
Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#5) to map
cryosparc_P26_J402_011_volume_map_sharp.mrc (#4) using 2539 atoms
average map value = 0.0267, steps = 48
shifted from previous position = 0.0131
rotated from previous position = 0.00744 degrees
atoms outside contour = 1811, contour level = 0.0343
> transparency #4.1 50
> view matrix models #5,1,0,0,-0.92563,0,1,0,-1.9541,0,0,1,-5.7241
> fitmap sel inMap #4 moveWholeMolecules false
Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#5) to map
cryosparc_P26_J402_011_volume_map_sharp.mrc (#4) using 2539 atoms
average map value = 0.0267, steps = 56
shifted from previous position = 1.45
rotated from previous position = 0.00861 degrees
atoms outside contour = 1812, contour level = 0.0343
> fitmap sel inMap #4 moveWholeMolecules false
Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#5) to map
cryosparc_P26_J402_011_volume_map_sharp.mrc (#4) using 2539 atoms
average map value = 0.0267, steps = 28
shifted from previous position = 0.00957
rotated from previous position = 0.0268 degrees
atoms outside contour = 1811, contour level = 0.0343
> select add #5
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 2 models selected
> select subtract #5
Nothing selected
> ui tool show "Show Sequence Viewer"
> sequence chain #5/M
Alignment identifier is 5/M
> select #5/M:5
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #5/M:5
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #5/M:5-8
32 atoms, 34 bonds, 4 residues, 1 model selected
> select #5/M:6
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/M:6
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select ::name="ILE"
4536 atoms, 4011 bonds, 567 residues, 4 models selected
> toolshed show
Downloading bundle ChimeraX_PhenixUI-1.3.7-py3-none-any.whl
Installed ChimeraX-PhenixUI (1.3.7)
> swapaa #5/M:6 ile
Using Dunbrack library
RAD54-J402_m1_real_space_refined_001.pdb #5/M VAL 6: phi -104.4, psi 112.3
trans
Density criteria with multiple volume models open;
Need to specify one to use via 'density' keyword.
> swapaa #5/M:6 ile`
Using Dunbrack library
RAD54-J402_m1_real_space_refined_001.pdb #5/M VAL 6: phi -104.4, psi 112.3
trans
Dunbrack rotamer library does not support ILE`
> swapaa #5/M:6 ile
Using Dunbrack library
RAD54-J402_m1_real_space_refined_001.pdb #5/M VAL 6: phi -104.4, psi 112.3
trans
Density criteria with multiple volume models open;
Need to specify one to use via 'density' keyword.
> swapaa #5/M:6 ile
Using Dunbrack library
RAD54-J402_m1_real_space_refined_001.pdb #5/M VAL 6: phi -104.4, psi 112.3
trans
Density criteria with multiple volume models open;
Need to specify one to use via 'density' keyword.
> swapaa #5/M:6 ile
Using Dunbrack library
RAD54-J402_m1_real_space_refined_001.pdb #5/M VAL 6: phi -104.4, psi 112.3
trans
Density criteria with multiple volume models open;
Need to specify one to use via 'density' keyword.
> swapaa #5/M:6 ile density #4
Using Dunbrack library
RAD54-J402_m1_real_space_refined_001.pdb #5/M VAL 6: phi -104.4, psi 112.3
trans
Applying ILE rotamer (chi angles: 59.9 85.2) to
RAD54-J402_m1_real_space_refined_001.pdb #5/M ILE 6
> select #5/M
69 atoms, 72 bonds, 8 residues, 1 model selected
> fitmap sel inMap #4 moveWholeMolecules false
Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#5) to map
cryosparc_P26_J402_011_volume_map_sharp.mrc (#4) using 69 atoms
average map value = 0.05783, steps = 44
shifted from previous position = 1.34
rotated from previous position = 1.09 degrees
atoms outside contour = 26, contour level = 0.0343
> select #5/A
2471 atoms, 2510 bonds, 1 pseudobond, 317 residues, 2 models selected
> fitmap sel inMap #4 moveWholeMolecules false
Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#5) to map
cryosparc_P26_J402_011_volume_map_sharp.mrc (#4) using 2471 atoms
average map value = 0.1065, steps = 52
shifted from previous position = 1.46
rotated from previous position = 0.00296 degrees
atoms outside contour = 426, contour level = 0.0343
> select add #5
15529 atoms, 15811 bonds, 6 pseudobonds, 1962 residues, 2 models selected
> select subtract #5
Nothing selected
> swapaa #5/M:4 lys density #4
Using Dunbrack library
RAD54-J402_m1_real_space_refined_001.pdb #5/M VAL 4: phi -127.5, psi 139.0
trans
Applying LYS rotamer (chi angles: -176.9 174.8 72.5 69.2) to
RAD54-J402_m1_real_space_refined_001.pdb #5/M LYS 4
> show #!5 atoms
> hide #!5 atoms
> select #5/M
71 atoms, 74 bonds, 8 residues, 1 model selected
> show sel atoms
> swapaa #5/M:3 pro density #4
Using Dunbrack library
RAD54-J402_m1_real_space_refined_001.pdb #5/M LYS 3: phi none, psi 134.6 trans
Applying PRO rotamer (chi angles: 27.0 -34.6) to
RAD54-J402_m1_real_space_refined_001.pdb #5/M PRO 3
> swapaa #5/M:9 gly density #4
Using Dunbrack library
Swapping RAD54-J402_m1_real_space_refined_001.pdb #5/M PHE 9 to GLY
> swapaa #5/M:10 arg density #4
Using Dunbrack library
RAD54-J402_m1_real_space_refined_001.pdb #5/M LYS 10: phi -99.9, psi none
trans
Applying ARG rotamer (chi angles: -83.1 81.9 69.8 -178.0) to
RAD54-J402_m1_real_space_refined_001.pdb #5/M ARG 10
> view matrix models #5,1,0,0,-0.47913,0,1,0,-1.925,0,0,1,-6.0718
> select #A,M
Expected an objects specifier or a keyword
> select #5/A,M
2535 atoms, 2577 bonds, 1 pseudobond, 325 residues, 2 models selected
> fitmap sel inMap #4 moveWholeMolecules false
Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#5) to map
cryosparc_P26_J402_011_volume_map_sharp.mrc (#4) using 2535 atoms
average map value = 0.1055, steps = 64
shifted from previous position = 0.574
rotated from previous position = 0.016 degrees
atoms outside contour = 440, contour level = 0.0343
> select add #5
15524 atoms, 15806 bonds, 6 pseudobonds, 1962 residues, 2 models selected
> select subtract #5
Nothing selected
> ui tool show "Local EM Fitting"
Populating font family aliases took 71 ms. Replace uses of missing font family
"Times" with one that exists to avoid this cost.
Must specify a resolution value for the full map
> select #5/M:3
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> ui tool show Rotamers
> select #5/M:10
11 atoms, 10 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel ARG rotLib Dunbrack
RAD54-J402_m1_real_space_refined_001.pdb #5/M ARG 10: phi -99.9, psi none
trans
Changed 648 bond radii
> swapaa #!5/M:10 ARG criteria 5 rotLib Dunbrack retain false
Using Dunbrack library
RAD54-J402_m1_real_space_refined_001.pdb #!5/M ARG 10: phi -99.9, psi none
trans
Applying ARG rotamer (chi angles: -176.9 176.3 178.8 -179.4) to
RAD54-J402_m1_real_space_refined_001.pdb #!5/M ARG 10
> swapaa interactive sel ARG rotLib Dunbrack
RAD54-J402_m1_real_space_refined_001.pdb #5/M ARG 10: phi -99.9, psi none
trans
Changed 648 bond radii
> select #5/M:4
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel LYS rotLib Dunbrack
RAD54-J402_m1_real_space_refined_001.pdb #5/M LYS 4: phi -127.5, psi 139.0
trans
Changed 438 bond radii
> swapaa #!5/M:4 LYS criteria 1 rotLib Dunbrack retain false
Using Dunbrack library
RAD54-J402_m1_real_space_refined_001.pdb #!5/M LYS 4: phi -127.5, psi 139.0
trans
Applying LYS rotamer (chi angles: -64.2 -177.9 -179.5 179.7) to
RAD54-J402_m1_real_space_refined_001.pdb #!5/M LYS 4
> select #5/M
64 atoms, 67 bonds, 8 residues, 1 model selected
> fitmap sel inMap #4 moveWholeMolecules false
Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#5) to map
cryosparc_P26_J402_011_volume_map_sharp.mrc (#4) using 64 atoms
average map value = 0.06077, steps = 48
shifted from previous position = 0.101
rotated from previous position = 2.24 degrees
atoms outside contour = 23, contour level = 0.0343
> select #5/M:10
11 atoms, 10 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel ARG rotLib Dunbrack
RAD54-J402_m1_real_space_refined_001.pdb #5/M ARG 10: phi -99.9, psi none
trans
Changed 648 bond radii
> view matrix models #5,1,0,0,-0.36351,0,1,0,-2.6595,0,0,1,-5.3788
> select #5/A,M
2535 atoms, 2577 bonds, 1 pseudobond, 325 residues, 2 models selected
> fitmap sel inMap #4 moveWholeMolecules false
Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#5) to map
cryosparc_P26_J402_011_volume_map_sharp.mrc (#4) using 2535 atoms
average map value = 0.1054, steps = 72
shifted from previous position = 1.01
rotated from previous position = 0.0195 degrees
atoms outside contour = 446, contour level = 0.0343
> select add #5
15524 atoms, 15806 bonds, 6 pseudobonds, 1962 residues, 2 models selected
> select subtract #5
Nothing selected
> select #5/M:10
11 atoms, 10 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel ARG rotLib Dunbrack
RAD54-J402_m1_real_space_refined_001.pdb #5/M ARG 10: phi -99.9, psi none
trans
Changed 648 bond radii
> select add #5
15524 atoms, 15806 bonds, 6 pseudobonds, 1962 residues, 2 models selected
> select subtract #5
Nothing selected
> color zone #4 near #5 distance 4.38
> transparency #4.1 0
> transparency #4.1 50
> hide #!5 models
> hide #!4 models
> show #!6 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 surfaces
> swapaa #3/P:3 lys density #6
Using Dunbrack library
newPDBfit-coot-10_real_space_refined_002.pdb #3/P LYS 3: phi none, psi -83.0
trans
Applying LYS rotamer (chi angles: 69.5 85.2 -93.8 -177.2) to newPDBfit-
coot-10_real_space_refined_002.pdb #3/P LYS 3
> select #3/P:3
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel LYS rotLib Dunbrack
newPDBfit-coot-10_real_space_refined_002.pdb #3/P LYS 3: phi none, psi -83.0
trans
Changed 486 bond radii
> swapaa #!3/P:3 LYS criteria 20 rotLib Dunbrack retain false
Using Dunbrack library
newPDBfit-coot-10_real_space_refined_002.pdb #!3/P LYS 3: phi none, psi -83.0
trans
Applying LYS rotamer (chi angles: 65.9 -178.1 173.2 66.9) to newPDBfit-
coot-10_real_space_refined_002.pdb #!3/P LYS 3
> select add #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected
> select subtract #3
13 models selected
> ui tool show "Local EM Fitting"
Must specify exactly two half maps for fitting
[Repeated 1 time(s)]No part of model for specifying search center is displayed
[Repeated 1 time(s)]
> marker #8 position 123.064,92.5207,108.869 radius 82.2268 color 100,65,0,50
> phenix emplaceLocal #3 mapData #6 resolution 2.5 center
> 123.064,92.5207,108.869 showSharpenedMap false applySymmetry false
Could not find Phenix installation in /Users/sz140275local, /Applications.
Use "phenix location" command to specify the location of your Phenix
installation.
The value you give to 'phenix location' needs to be the full path to
the top-level folder that Phenix created when it was installed.
You can use 'phenix location browse' in order to use a file browser
to specify the installation location.
> hide #!3 models
> show #!2 models
> hide #!6 models
> select #2/D,P
2539 atoms, 2580 bonds, 1 pseudobond, 325 residues, 2 models selected
> collor bfactor sel
Unknown command: collor bfactor sel
> color bfactor sel
2539 atoms, 325 residues, atom bfactor range 52.2 to 170
> select #2
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 2 models selected
> color bfactor sel
15528 atoms, 1962 residues, atom bfactor range 52.2 to 242
> view matrix models #2,1,0,0,12.319,0,1,0,-3.9459,0,0,1,4.8367
> select #2
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 2 models selected
> color sel wheat
> select #2/D,P
2539 atoms, 2580 bonds, 1 pseudobond, 325 residues, 2 models selected
> color bfactor sel
2539 atoms, 325 residues, atom bfactor range 52.2 to 170
> select #2/D:ATP*
31 atoms, 33 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/D:Mg*
2 atoms, 2 residues, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> select add #2
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 2 models selected
> select subtract #2
Nothing selected
> select #2/P
68 atoms, 71 bonds, 8 residues, 1 model selected
> show sel atoms
> select #2/P:3,10
18 atoms, 16 bonds, 2 residues, 1 model selected
> hide sel atoms
> select add #2
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 2 models selected
> select subtract #2
Nothing selected
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
> RAD54/BRCA2bfactor.tif" width 841 height 750 supersample 3
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> show #!3 models
> select #3/D
2471 atoms, 2509 bonds, 1 pseudobond, 317 residues, 2 models selected
> color sel royal blue
> color sel dodger blue
> color sel royal blue
> select #3/P
68 atoms, 71 bonds, 8 residues, 1 model selected
> color sel red
> select #3/D:Mg*
2 atoms, 2 residues, 1 model selected
> show sel atoms
> color sel black
> select #3/D:ATP*
31 atoms, 33 bonds, 1 residue, 1 model selected
> color sel black
> select #3/C:ATP*,MG*
33 atoms, 33 bonds, 3 residues, 1 model selected
> color sel black
> select #3/C:Mg*
2 atoms, 2 residues, 1 model selected
> show sel atoms
> select add #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 2 models selected
> select subtract #3
13 models selected
> select #3/E
2438 atoms, 2476 bonds, 1 pseudobond, 314 residues, 2 models selected
> show sel atoms
> hide sel atoms
> color sel wheat
> select add #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected
> select subtract #3
13 models selected
> show #!6 models
> hide #!6 models
> show #!6 models
> color zone #6 near #3 distance 4.38
> transparency #3.2-14#6.1 0
> transparency #3.2-14#6.1 50
> volume #6 level 0.04563
> color zone #6 near #3 distance 4.38
> transparency #3.2-14#6.1 0
> transparency #3.2-14#6.1 50
> hide #!6 models
Window position QRect(974,990 654x459) outside any known screen, using primary
screen
> show #!6 models
> open "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
> structure BRCA2 07072025/cryosparc_P26_J362_012_volume_map.mrc"
Opened cryosparc_P26_J362_012_volume_map.mrc as #8, grid size 336,336,336,
pixel 0.73, shown at level 0.0236, step 2, values float32
> hide #!6 models
> color zone #8 near #3 distance 4.38
> transparency #3.2-14#8.1 0
> transparency #3.2-14#8.1 50
> surface dust #8 size 7.3
> swapaa #3/P:9 phe density #8
Using Dunbrack library
newPDBfit-coot-10_real_space_refined_002.pdb #3/P PHE 9: phi -81.6, psi 168.3
trans
Applying PHE rotamer (chi angles: 60.6 108.6) to newPDBfit-
coot-10_real_space_refined_002.pdb #3/P PHE 9
> size sticksrad 0.7
Expected a keyword
> size sticksrad 0.7
Expected a keyword
> size stickRadius 0.7
Changed 55012 bond radii
> size stickRadius 0.4
Changed 55012 bond radii
> select #3/P
68 atoms, 71 bonds, 8 residues, 1 model selected
> color bfactor sel
68 atoms, 8 residues, 1 surfaces, atom bfactor range 104 to 145
> select add #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected
> select subtract #3
13 models selected
> color sel red
> select #3/P
68 atoms, 71 bonds, 8 residues, 1 model selected
> color sel red
> select add #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected
> select subtract #3
13 models selected
> select #3/Q
68 atoms, 71 bonds, 8 residues, 1 model selected
> color sel wheat
> select add #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected
> select subtract #3
13 models selected
> color zone #8 near #3 distance 4.38
> transparency #3.2-14#8.1 0
> transparency #3.2-14#8.1 50
> select #3/Q
68 atoms, 71 bonds, 8 residues, 1 model selected
> hide sel atoms
> select add #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected
> select subtract #3
13 models selected
> volume #6 style mesh
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
> RAD54/BRCA2bPeptide.tif" width 841 height 709 supersample 3
> select #3/P:3,10
18 atoms, 16 bonds, 2 residues, 1 model selected
> hide sel atoms
> select add #3
15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected
> select subtract #3
13 models selected
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
> RAD54/BRCA2bPeptide.tif" width 841 height 709 supersample 3
> open "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
> structure RAD54B 07072025/cryosparc_P26_J410_011_volume_map_sharp.mrc"
Opened cryosparc_P26_J410_011_volume_map_sharp.mrc as #9, grid size
336,336,336, pixel 0.73, shown at level 0.032, step 2, values float32
> hide #!3 models
> hide #!8 models
> surface dust #9 size 7.3
> open "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
> structure RAD54B 07072025/RAD54-J402_m4_real_space_refined_000.pdb"
Chain information for RAD54-J402_m4_real_space_refined_000.pdb #10
---
Chain | Description
A B C D E F | No description available
M | No description available
N O P Q | No description available
R | No description available
X | No description available
> style #!10 stick
Changed 15512 atom styles
> hide #!10 atoms
> show #!10 cartoons
> transparency #9.1 50
> open "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
> structure BRCA2 07072025/BRCA2_m4_real_space_refined_000.pdb"
Chain information for BRCA2_m4_real_space_refined_000.pdb #11
---
Chain | Description
A B C D E F | No description available
M N O P Q R | No description available
X | No description available
> hide #!11 models
> select #9/X
Nothing selected
> select #10/X
360 atoms, 395 bonds, 18 residues, 1 model selected
> color sel lime
> select #10/A,B,C,D,E,F,G:ATP*
Nothing selected
> select #10/A,B,C,D,E,F,G:AMPPNP*
Nothing selected
> select #10/A,B,C,D,E,F,G:ANP*
155 atoms, 165 bonds, 5 residues, 1 model selected
> color sel blue
> show sel atoms
> select #10/A,B,C,D,E,F,G:Ca*
10 atoms, 10 residues, 1 model selected
> color sel blue
> show sel atoms
[Repeated 1 time(s)]
> select add #10
15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 2 models selected
> select subtract #10
Nothing selected
> select #10/M,N,O,P,Q,R,S
359 atoms, 375 bonds, 45 residues, 1 model selected
> color sel red
> show sel atoms
> select #10/X
360 atoms, 395 bonds, 18 residues, 1 model selected
> hide sel cartoons
> show sel atoms
> select add #10
15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 2 models selected
> select subtract #10
Nothing selected
> hide #!9 models
> show #!9 models
> color #10/C wheat
> select add #10
15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 2 models selected
> color zone #9 near sel & #10 distance 4.38
> transparency #9.1 0
> transparency #9.1 50
> select subtract #10
Nothing selected
> select #10/A,B,C,D,E,F,G
14793 atoms, 15021 bonds, 6 pseudobonds, 1899 residues, 2 models selected
> hide sel cartoons
> select add #10
15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 2 models selected
> select subtract #10
Nothing selected
> volume #6 level 0.05
> volume #9 level 0.035
> color zone #9 near #10 distance 4.38
> transparency #9.1 0
> transparency #9.1 50
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
> RAD54/RAD54SupB.tif" width 841 height 709 supersample 3
> select #10/C
2471 atoms, 2509 bonds, 1 pseudobond, 317 residues, 2 models selected
> hide #!9 models
> select add #10
15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 2 models selected
> select subtract #10
Nothing selected
> select #10/A,B,C,D,E,F,G
14793 atoms, 15021 bonds, 6 pseudobonds, 1899 residues, 2 models selected
> show sel cartoons
> select #10/A,B,D,E,F,G
12322 atoms, 12512 bonds, 5 pseudobonds, 1582 residues, 2 models selected
> show sel surfaces
> select add #10
15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 7 models selected
> select subtract #10
5 models selected
> select #10/C:ANP*
31 atoms, 33 bonds, 1 residue, 1 model selected
> color sel blue
> select #10/C:Ca*
2 atoms, 2 residues, 1 model selected
> color sel blue
> size stickRadius 0.7
Changed 86646 bond radii
> size stickRadius 0.4
Changed 86646 bond radii
> size stickRadius 0.25
Changed 86646 bond radii
> size atomRadius 0.25
Changed 85392 atom radii
> size atomRadius 0.5
Changed 85392 atom radii
> select #10/A,B,C:Ca*
6 atoms, 6 residues, 1 model selected
> size atomRadius 0.5
Changed 85392 atom radii
> size atomRadius 1
Changed 85392 atom radii
> size ballScale 1
Changed 6 ball scales
> size ballScale 2
Changed 6 ball scales
> size sel ballScale 2
Changed 1 ball scales
> size sel atomRadius 1
Changed 6 atom radii
> size sel atomRadius 3
Changed 6 atom radii
> select #10/A,B,C:Ca*
6 atoms, 6 residues, 1 model selected
> size sel atomRadius 1
Changed 6 atom radii
> size sel atomRadius 10
Changed 6 atom radii
> size sel ballScale 10
Changed 1 ball scales
> style sel sphere
Changed 6 atom styles
> size sel ballScale 1
Changed 1 ball scales
> select #10/A,B,C:Ca*
6 atoms, 6 residues, 1 model selected
> size sel ballScale 0.2
Changed 1 ball scales
> size sel atomRadius 1
Changed 6 atom radii
> select add #10
15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 2 models selected
> select subtract #10
5 models selected
> select #10/A,B,C:ATP*
Nothing selected
> select #10/A,B,C:ANP*
93 atoms, 99 bonds, 3 residues, 1 model selected
> size stickRadius 0.4
Changed 86646 bond radii
> select add #10
15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 2 models selected
> select subtract #10
5 models selected
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
> RAD54/RAD54SUPC.tif" width 841 height 709 supersample 3
> ui tool show "Show Sequence Viewer"
> sequence chain #11/O
Alignment identifier is 11/O
> show #!9 models
> ui mousemode right translate
> hide #!9 models
> select #11/O:3
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #11/O:3
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
7 atoms, 7 bonds, 1 residue, 1 model selected
> select add #10
15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 2 models selected
> select subtract #10
5 models selected
> show #!9 models
> select #9
2 models selected
> select subtract #9
Nothing selected
> hide #!9 models
> select #10/O:10
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #10/O:9
4 atoms, 3 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #10/O
Alignment identifier is 10/O
> select add #10
15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 2 models selected
> select subtract #10
5 models selected
> show #!9 models
> hide #!9 models
> swapaa #10/O:10 arg density #9
Using Dunbrack library
RAD54-J402_m4_real_space_refined_000.pdb #10/O ARG 10: phi -128.2, psi none
trans
Applying ARG rotamer (chi angles: -83.1 81.9 69.8 -178.0) to
RAD54-J402_m4_real_space_refined_000.pdb #10/O ARG 10
> show #!9 models
> swapaa #10/O:10 arg density #9
Using Dunbrack library
RAD54-J402_m4_real_space_refined_000.pdb #10/O ARG 10: phi -128.2, psi none
trans
Applying ARG rotamer (chi angles: -83.1 81.9 69.8 -178.0) to
RAD54-J402_m4_real_space_refined_000.pdb #10/O ARG 10
> swapaa #10/O:10 val density #9
Using Dunbrack library
RAD54-J402_m4_real_space_refined_000.pdb #10/O ARG 10: phi -128.2, psi none
trans
Applying VAL rotamer (chi angles: 65.5) to
RAD54-J402_m4_real_space_refined_000.pdb #10/O VAL 10
> swapaa #10/O:10 val density #9
Using Dunbrack library
RAD54-J402_m4_real_space_refined_000.pdb #10/O VAL 10: phi -128.2, psi none
trans
Applying VAL rotamer (chi angles: 65.5) to
RAD54-J402_m4_real_space_refined_000.pdb #10/O VAL 10
> swapaa #10/O:10 arg density #9
Using Dunbrack library
RAD54-J402_m4_real_space_refined_000.pdb #10/O VAL 10: phi -128.2, psi none
trans
Applying ARG rotamer (chi angles: -78.6 73.8 -179.4 85.1) to
RAD54-J402_m4_real_space_refined_000.pdb #10/O ARG 10
> select #10/O:10
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select add #10
15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 2 models selected
> select subtract #10
5 models selected
> ui mousemode right zoom
> select #10/A,B,C,D,E,F,G:Ca*
10 atoms, 10 residues, 1 model selected
> color sel black
> select #10/A,B,C,D,E,F,G:ANP*
155 atoms, 165 bonds, 5 residues, 1 model selected
> color sel black
> select #10/A,C,E,F
9851 atoms, 10003 bonds, 4 pseudobonds, 1265 residues, 2 models selected
> color sel wheat
> select #10/B,D,F
7380 atoms, 7494 bonds, 3 pseudobonds, 948 residues, 2 models selected
> color sel royal blue
> select #10/A,C,E,G
7413 atoms, 7527 bonds, 3 pseudobonds, 951 residues, 2 models selected
> color sel wheat
> volume #9 color #feefdd80
> volume #9 color #fef3d780
> select add #10
15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 4 models selected
> select subtract #10
5 models selected
> select add #9
2 models selected
> color sel misty rose
> select subtract #9
Nothing selected
> select add #9
2 models selected
> select subtract #9
Nothing selected
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> select add #10
15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 2 models selected
> hide sel surfaces
> select subtract #10
5 models selected
> select add #9
2 models selected
> color zone #9 near #10 distance 4.38
> select subtract #9
Nothing selected
> hide #!10 models
> show #!10 models
> hide #!9 models
> select #10/M,N,O,P,Q,R,S:1O
Nothing selected
> select #10/M,N,O,P,Q,R,S:10
55 atoms, 50 bonds, 5 residues, 1 model selected
> hide sel atoms
> select add #10
15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 2 models selected
> select subtract #10
5 models selected
> show #!9 models
> hide #!10 models
> ui mousemode right translate
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
> RAD54/RAD54BfigA.tif" width 841 height 709 supersample 3
> show #!10 models
> transparency #9.1#10.2-6 0
> transparency #9.1#10.2-6 50
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> select #10/D:85,89
22 atoms, 22 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel orange
> color zone #9 near sel & #10 distance 4.38
> select add #10
15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 3 models selected
> select subtract #10
5 models selected
> color zone #9 near #10 distance 4.38
> transparency #9.1#10.2-6 0
> transparency #9.1#10.2-6 50
> select #10/C:85,89
22 atoms, 22 bonds, 2 residues, 1 model selected
> show sel atoms
> select #10/D:85,89
22 atoms, 22 bonds, 2 residues, 1 model selected
> select #10/E:85,89
22 atoms, 22 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel orange
> select add #10
15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 3 models selected
> select subtract #10
5 models selected
> color zone #9 near #10 distance 4.38
> transparency #9.1#10.2-6 0
> transparency #9.1#10.2-6 50
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
> RAD54/RAD54BfigB.tif" width 841 height 709 supersample 3
> hide #!9 models
> show #!9 models
> ui mousemode right zoom
> ui mousemode right translate
> hide #!9 models
> select #10/E
2471 atoms, 2509 bonds, 1 pseudobond, 317 residues, 2 models selected
> color sel wheat
> hide sel atoms
> select add #10
15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 3 models selected
> select subtract #10
5 models selected
> show #!9 models
> color zone #9 near #10 distance 4.38
> transparency #9.1#10.2-6 0
> transparency #9.1#10.2-6 50
> cartoon style coil width 2 thickness 1
> cartoon style coil width 2 thickness 0.5
> hide #!9 models
> select #10/Q
64 atoms, 67 bonds, 8 residues, 1 model selected
> color sel wheat
> select add #10
15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 2 models selected
> select subtract #10
5 models selected
> show #!9 models
> color zone #9 near #10 distance 4.38
> transparency #9.1#10.2-6 0
> transparency #9.1#10.2-6 50
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
> RAD54/RAD54BfigD.tif" width 841 height 709 supersample 3
> volume #9 level 0.02294
> color zone #9 near #10 distance 4.38
> transparency #9.1#10.2-6 0
> transparency #9.1#10.2-6 50
> hide #!9 models
> select clear
> select #10/P:9
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #10/P:8@CA
1 atom, 1 residue, 1 model selected
> select #10/P:9
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #10/P:10
11 atoms, 10 bonds, 1 residue, 1 model selected
> show #!9 models
> select add #10
15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 2 models selected
> select subtract #10
5 models selected
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
> RAD54/RAD54B.cxs"
——— End of log from Thu Jul 10 10:47:21 2025 ———
opened ChimeraX session
> close #2-3,5-11
> open "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
> structure BRCA2 07072025/BRCA2_m4_real_space_refined_000.pdb"
> "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
> structure BRCA2 07072025/cryosparc_P26_J362_012_volume_map_sharp.mrc"
> "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
> structure BRCA2 07072025/cryosparc_P26_J362_012_volume_map.mrc"
Chain information for BRCA2_m4_real_space_refined_000.pdb #1
---
Chain | Description
A B C D E F | No description available
M N O P Q R | No description available
X | No description available
Opened cryosparc_P26_J362_012_volume_map_sharp.mrc as #2, grid size
336,336,336, pixel 0.73, shown at level 0.0403, step 2, values float32
Opened cryosparc_P26_J362_012_volume_map.mrc as #3, grid size 336,336,336,
pixel 0.73, shown at level 0.0236, step 2, values float32
> select add #2
2 models selected
Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 2 maps.
> surface dust #2 size 7.3
> select add #3
4 models selected
> select subtract #2
2 models selected
> surface dust #3 size 7.3
> hide #!2 models
> hide #!3 models
> select subtract #3
Nothing selected
> select add #1
15848 atoms, 15843 bonds, 6 pseudobonds, 2252 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> show sel cartoons
> select #1/A,C,E
7413 atoms, 7528 bonds, 3 pseudobonds, 951 residues, 2 models selected
> color sel royal blue
> select #1/B,D,F
7380 atoms, 7494 bonds, 3 pseudobonds, 948 residues, 2 models selected
> color sel wheat
> select #1/X
360 atoms, 395 bonds, 18 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> style sel stick
Changed 360 atom styles
> color sel dark green
> select add #1
15848 atoms, 15843 bonds, 6 pseudobonds, 2252 residues, 2 models selected
> select subtract #1
Nothing selected
> color sel #1/M,N,O,P,Q,R,S
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel #1/M,N,O,P,Q,R
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #1/M,N,O,P,Q,R red
> show atoms
> hide atoms
> select #1/M,N,O,P,Q,R
408 atoms, 426 bonds, 48 residues, 1 model selected
> show sel atoms
> select #1/M,N,O,P,Q,R:3,10
108 atoms, 96 bonds, 12 residues, 1 model selected
> hide sel atoms
> select #1/A,C,E:ANP*
93 atoms, 99 bonds, 3 residues, 1 model selected
> select #1/A,C,E:ANP*,Ca*
99 atoms, 99 bonds, 9 residues, 1 model selected
> color sel black
> color sel dark grey
> show sel atoms
> select #1/B,D,F:ANP*,Ca*
66 atoms, 66 bonds, 6 residues, 1 model selected
> color sel dark grey
> show sel atoms
> select add #1
15848 atoms, 15843 bonds, 6 pseudobonds, 2252 residues, 2 models selected
> select subtract #1
Nothing selected
> SEL #1/X
Unknown command: SEL #1/X
> select #1/X
360 atoms, 395 bonds, 18 residues, 1 model selected
> show sel atoms
> select add #1
15848 atoms, 15843 bonds, 6 pseudobonds, 2252 residues, 2 models selected
> select subtract #1
Nothing selected
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> volume #2 level 0.05157
> show #!1 models
> color zone #2 near #1 distance 4.38
> transparency #2.1 50
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select add #1
15848 atoms, 15843 bonds, 6 pseudobonds, 2252 residues, 2 models selected
> color zone #2 near sel & #1 distance 4.38
[Repeated 1 time(s)]
> select subtract #1
Nothing selected
> volume #2 level 0.04484
> select #1/B,D,F
7380 atoms, 7494 bonds, 3 pseudobonds, 948 residues, 2 models selected
> hide sel atoms
[Repeated 2 time(s)]
> select #1/B,D,F:ANP*,Ca*
66 atoms, 66 bonds, 6 residues, 1 model selected
> show sel atoms
> color zone #2 near sel & #1 distance 4.38
[Repeated 1 time(s)]
> select add #1
15848 atoms, 15843 bonds, 6 pseudobonds, 2252 residues, 2 models selected
> select subtract #1
Nothing selected
> select add #1
15848 atoms, 15843 bonds, 6 pseudobonds, 2252 residues, 2 models selected
> color zone #2 near sel & #1 distance 4.38
> select subtract #1
Nothing selected
> color #2 #b7bfb9ff models
> volume #2 level 0.0583
> ui tool show "Color Zone"
> color zone #2 near #1 distance 4
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select #1/A,B,C,D,E,F
14793 atoms, 15022 bonds, 6 pseudobonds, 1899 residues, 2 models selected
> show sel atoms
> style sel stick
Changed 14793 atom styles
> hide sel atoms
> color zone #2 near #1 distance 4
> select add #1
15848 atoms, 15843 bonds, 6 pseudobonds, 2252 residues, 2 models selected
> select subtract #1
Nothing selected
> show #!2 models
> color zone #2 near #1 distance 4
[Repeated 1 time(s)]
> transparency #2.1 50
> select #1/B,D,F
7380 atoms, 7494 bonds, 3 pseudobonds, 948 residues, 2 models selected
> show sel atoms
> select #1/A,C,E
7413 atoms, 7528 bonds, 3 pseudobonds, 951 residues, 2 models selected
> show sel atoms
> surface dust #2 size 7.3
[Repeated 3 time(s)]
> select add #1
15848 atoms, 15843 bonds, 6 pseudobonds, 2252 residues, 2 models selected
> select subtract #1
Nothing selected
> hide #!2 models
> show #!2 models
> hide #!1 models
> surface dust #2 size 7.3
[Repeated 1 time(s)]
> volume #2 level 0.06579
> show #!1 models
> transparency #2.1 50
> volume #2 level 0.04183
> color zone #2 near #1 distance 4
> color single #2
> color #2 light grey
> color zone #2 near #1 distance 4
> color single #2
[Repeated 1 time(s)]
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> color zone #3 near #1 distance 4.38
> transparency #3.1 50
> color #3 #b8bfb3ff models
> color zone #3 near #1 distance 4.38
> color single #3
> color zone #3 near #1 distance 3.99
[Repeated 1 time(s)]
> color single #3
> color zone #3 near #1 distance 3.99
[Repeated 1 time(s)]
> color single #3
> color #3 light grey
> color zone #3 near #1 distance 4.38
[Repeated 1 time(s)]
> color single #3
> color zone #3 near #1 distance 3.99
> color zone #2 near #1 distance 4
> color single #3
> color zone #2 near #1 distance 4
> hide #!3 models
> show #!2 models
> color single #3
> color single #2
> color zone #2 near #1 distance 4
> hide #!2 models
> select #1
15848 atoms, 15843 bonds, 6 pseudobonds, 2252 residues, 2 models selected
> select #1/C
2471 atoms, 2509 bonds, 1 pseudobond, 317 residues, 2 models selected
> select #1/C
2471 atoms, 2509 bonds, 1 pseudobond, 317 residues, 2 models selected
> color sel royal blue
> color zone #2 near sel distance 4
> show #!2 models
> select add #1
15848 atoms, 15843 bonds, 6 pseudobonds, 2252 residues, 2 models selected
> select subtract #1
Nothing selected
> select #1/O
68 atoms, 71 bonds, 8 residues, 1 model selected
> color zone #2 near sel distance 4
> select #1/O,C
2539 atoms, 2580 bonds, 1 pseudobond, 325 residues, 2 models selected
> color zone #2 near sel distance 4
> select add #1
15848 atoms, 15843 bonds, 6 pseudobonds, 2252 residues, 2 models selected
> select subtract #1
Nothing selected
> select #1/O
68 atoms, 71 bonds, 8 residues, 1 model selected
> transparency #2.1 0
> transparency #2.1 50
> select #1/C
2471 atoms, 2509 bonds, 1 pseudobond, 317 residues, 2 models selected
> transparency #2.1 0
> select #1/O
68 atoms, 71 bonds, 8 residues, 1 model selected
> transparency #2.1 50
> select add #1
15848 atoms, 15843 bonds, 6 pseudobonds, 2252 residues, 2 models selected
> select subtract #1
Nothing selected
> select #1/C:ANP*
31 atoms, 33 bonds, 1 residue, 1 model selected
> color sel magenta
> select #1/C:Ca*
2 atoms, 2 residues, 1 model selected
> color sel magenta
> select add #1
15848 atoms, 15843 bonds, 6 pseudobonds, 2252 residues, 2 models selected
> select subtract #1
Nothing selected
> select #1/C:Ca*
2 atoms, 2 residues, 1 model selected
> select #1/A,B,C,D,E,F:Ca*,ANP*
165 atoms, 165 bonds, 15 residues, 1 model selected
> color sel magenta
> color zone #2 near sel distance 4
> select #1/A,B,C,D,E,F
14793 atoms, 15022 bonds, 6 pseudobonds, 1899 residues, 2 models selected
> color zone #2 near sel distance 4
> transparency #2.1 0
> transparency #2.1 50
> select add #1
15848 atoms, 15843 bonds, 6 pseudobonds, 2252 residues, 2 models selected
> select subtract #1
Nothing selected
> select #1/A,B,C,D,E,F
14793 atoms, 15022 bonds, 6 pseudobonds, 1899 residues, 2 models selected
> select #1/A,B,C,D,E,F:85,89
132 atoms, 132 bonds, 12 residues, 1 model selected
> color sel orange
> select add #1
15848 atoms, 15843 bonds, 6 pseudobonds, 2252 residues, 2 models selected
> select subtract #1
Nothing selected
> open 8qqe
8qqe title:
Crystal structure of the complex between DMC1 and the PhePP domain of BRCA2
[more info...]
Chain information for 8qqe #4
---
Chain | Description | UniProt
A B | Meiotic recombination protein DMC1/LIM15 homolog | DMC1_HUMAN 2-340
C D | Breast cancer type 2 susceptibility protein | BRCA2_HUMAN 1398-1417 2398-2417
Non-standard residues in 8qqe #4
---
CL — chloride ion
MG — magnesium ion
8qqe mmCIF Assemblies
---
1| author_defined_assembly
39 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> mmaker #4/B to #1/D
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker BRCA2_m4_real_space_refined_000.pdb, chain D (#1) with 8qqe, chain
B (#4), sequence alignment score = 1439.4
RMSD between 221 pruned atom pairs is 0.588 angstroms; (across all 247 pairs:
2.519)
> hide #!2 models
> select #1/A,B,C,D,E,F
14793 atoms, 15022 bonds, 6 pseudobonds, 1899 residues, 2 models selected
> hide sel atoms
> select #1/A,B,C,D,E,F:ANP*,Ca*
165 atoms, 165 bonds, 15 residues, 1 model selected
> show sel atoms
> select add #1
15848 atoms, 15843 bonds, 6 pseudobonds, 2252 residues, 2 models selected
> select subtract #1
Nothing selected
> open "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
> structure RAD54B 07072025/RAD54-J402_m4_real_space_refined_000.pdb"
Chain information for RAD54-J402_m4_real_space_refined_000.pdb #5
---
Chain | Description
A B C D E F | No description available
M | No description available
N O P Q | No description available
R | No description available
X | No description available
> mmaker #5 to #1
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker BRCA2_m4_real_space_refined_000.pdb, chain D (#1) with
RAD54-J402_m4_real_space_refined_000.pdb, chain B (#5), sequence alignment
score = 1612.8
RMSD between 314 pruned atom pairs is 0.198 angstroms; (across all 314 pairs:
0.198)
> hide #!4 models
> hide #!1 models
> hide #!5 atoms
> select add #5
15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 2 models selected
> show sel atoms
> hide sel atoms
> show sel cartoons
> select subtract #5
Nothing selected
> show #!1 models
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
> structure BRCA2 07072025/ForAlexPhePP.cxs"
> hide #!5 models
> show #!4 models
> select #1/A,B,C
7413 atoms, 7528 bonds, 3 pseudobonds, 951 residues, 2 models selected
> hide sel cartoons
> select #1/M,N,O
204 atoms, 213 bonds, 24 residues, 1 model selected
> hide sel cartoons
> select #1/A,B,C
7413 atoms, 7528 bonds, 3 pseudobonds, 951 residues, 2 models selected
> hide sel atoms
[Repeated 1 time(s)]
> select #1/M,N,O
204 atoms, 213 bonds, 24 residues, 1 model selected
> hide sel atoms
> select #1/X
360 atoms, 395 bonds, 18 residues, 1 model selected
> hide sel atoms
> select #1/F,R
2506 atoms, 2547 bonds, 1 pseudobond, 322 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select #4
4377 atoms, 4448 bonds, 5 pseudobonds, 564 residues, 4 models selected
> ~label (#!4 & sel) residues
> ~label (#!4 & sel) atoms
> select #4
4377 atoms, 4448 bonds, 5 pseudobonds, 564 residues, 4 models selected
> label offset
Missing "offset" keyword's argument
> label
> label #4
> label #4 offset
Missing "offset" keyword's argument
> ~label (#!4 & sel) residues
> label chain
Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword
> label models
> label models offset
Missing "offset" keyword's argument
> label models
> cartoon hide (#!4 & sel)
> cartoon (#!4 & sel)
> select subtract #4
Nothing selected
> select add #4
4377 atoms, 4448 bonds, 5 pseudobonds, 564 residues, 4 models selected
> select subtract #4
Nothing selected
> select #1/E:89
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/E:85
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select add #1
15848 atoms, 15843 bonds, 6 pseudobonds, 2252 residues, 2 models selected
> select subtract #1
Nothing selected
> select clear
[Repeated 1 time(s)]
> select #4/C:2403
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #4
4377 atoms, 4448 bonds, 5 pseudobonds, 564 residues, 4 models selected
> select subtract #4
Nothing selected
> select #4/C,D
141 atoms, 146 bonds, 18 residues, 1 model selected
> color sel purple
> select add #4
4377 atoms, 4448 bonds, 5 pseudobonds, 564 residues, 4 models selected
> select subtract #4
Nothing selected
> select #4/A:100-390
1756 atoms, 1785 bonds, 1 pseudobond, 226 residues, 2 models selected
> show sel surfaces
> hide sel surfaces
> select #4/B:100-390
1768 atoms, 1798 bonds, 1 pseudobond, 228 residues, 2 models selected
> show sel surfaces
> select add #4
4377 atoms, 4448 bonds, 5 pseudobonds, 564 residues, 5 models selected
> select subtract #4
2 models selected
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
> structure BRCA2 07072025/Brca2 xray vs cryo.cxs"
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
> structure BRCA2 07072025/BRCA2xrayVScryoEM.tif" width 786 height 694
> supersample 3
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
Alignment identifier is 4
Alignment identifier is 5
Alignment identifier is 5/M
Alignment identifier is 6
Alignment identifier is 5/R
> select #4/C,D
141 atoms, 146 bonds, 18 residues, 1 model selected
> select #4/C,D
141 atoms, 146 bonds, 18 residues, 1 model selected
> show sel atoms
> select add #4
4377 atoms, 4448 bonds, 5 pseudobonds, 564 residues, 4 models selected
> select subtract #4
2 models selected
> show #!3 models
> hide #!3 models
> show #!3 models
> transparency #3.1#4.3-4 50
> hide #!3 models
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
> structure BRCA2 07072025/Brca2 xray vs cryo.cxs"
> select #4/A:290:299
11 atoms, 9 bonds, 2 residues, 1 model selected
> select #1/X
360 atoms, 395 bonds, 18 residues, 1 model selected
> show sel cartoons
> color sel black
> select add #1
15848 atoms, 15843 bonds, 6 pseudobonds, 2252 residues, 2 models selected
> select subtract #1
Nothing selected
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
> structure BRCA2 07072025/BRCA2xrayVScryoEM2.tif" width 786 height 694
> supersample 3
> select #4/A:317:327
15 atoms, 13 bonds, 2 residues, 1 model selected
> select #4/A:317-327
83 atoms, 84 bonds, 11 residues, 1 model selected
> hide sel surfaces
[Repeated 1 time(s)]
> select add #4
4377 atoms, 4448 bonds, 5 pseudobonds, 564 residues, 5 models selected
> select subtract #4
2 models selected
> select add #4
4377 atoms, 4448 bonds, 5 pseudobonds, 564 residues, 4 models selected
> hide sel surfaces
> select subtract #4
2 models selected
> select add #4
4377 atoms, 4448 bonds, 5 pseudobonds, 564 residues, 4 models selected
> select subtract #4
2 models selected
> select #4/A
2306 atoms, 2338 bonds, 4 pseudobonds, 298 residues, 3 models selected
> select #4/A
2306 atoms, 2338 bonds, 4 pseudobonds, 298 residues, 3 models selected
> color sel aquamarine
> select add #4
4377 atoms, 4448 bonds, 5 pseudobonds, 564 residues, 5 models selected
> select subtract #4
2 models selected
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
> structure BRCA2 07072025/Brca2 xray vs cryo.cxs"
> close #5
> close #2-3
> open "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
> structure RAD54B 07072025/cryosparc_P26_J410_011_volume_map_sharp.mrc"
> "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
> structure RAD54B 07072025/cryosparc_P26_J410_011_volume_map.mrc"
Opened cryosparc_P26_J410_011_volume_map_sharp.mrc as #2.1, grid size
336,336,336, pixel 0.73, shown at level 0.032, step 2, values float32
Opened cryosparc_P26_J410_011_volume_map.mrc as #2.2, grid size 336,336,336,
pixel 0.73, shown at level 0.0225, step 2, values float32
> surface dust #2.1 size 7.3
> surface dust #2.2 size 7.3
> open "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
> structure RAD54B 07072025/RAD54-J402_m4_real_space_refined_000.pdb"
Chain information for RAD54-J402_m4_real_space_refined_000.pdb #3
---
Chain | Description
A B C D E F | No description available
M | No description available
N O P Q | No description available
R | No description available
X | No description available
> mmaker #1 to #3
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker RAD54-J402_m4_real_space_refined_000.pdb, chain B (#3) with
BRCA2_m4_real_space_refined_000.pdb, chain D (#1), sequence alignment score =
1612.8
RMSD between 314 pruned atom pairs is 0.198 angstroms; (across all 314 pairs:
0.198)
> select add #1
15848 atoms, 15843 bonds, 6 pseudobonds, 2252 residues, 2 models selected
> select subtract #1
Nothing selected
> select add #3
15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 2 models selected
> hide sel atoms
> show sel atoms
> hide sel atoms
> show sel cartoons
[Repeated 1 time(s)]
> mmaker #4/B to #3/D
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker RAD54-J402_m4_real_space_refined_000.pdb, chain D (#3) with 8qqe,
chain B (#4), sequence alignment score = 1439.4
RMSD between 222 pruned atom pairs is 0.604 angstroms; (across all 247 pairs:
2.534)
> select add #2.1
15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 4 models selected
> hide #!1 models
> hide #!2 models
> hide #!2.2 models
> hide #!3 models
> hide #!4 models
> select add #2
15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 7 models selected
> select subtract #2
15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 2 models selected
> show #!3 models
> show #!2 models
> color zone #2.1 near sel & #3 distance 4.38
> color #8/X drak green
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #3/X drak green
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #3/X dark green
> hide sel atoms
> show sel atoms
> hide sel cartoons
[Repeated 1 time(s)]
> hide sel atoms
> show sel atoms
> select #3/X
360 atoms, 395 bonds, 18 residues, 1 model selected
> style sel stick
Changed 360 atom styles
> show sel atoms
> color zone #2.1 near sel distance 4.38
> select #3/A,B,C,D,E,F
14793 atoms, 15021 bonds, 6 pseudobonds, 1899 residues, 2 models selected
> hide sel atoms
> select #3/A,B,C,D,E,F
14793 atoms, 15021 bonds, 6 pseudobonds, 1899 residues, 2 models selected
> show sel cartoons
> hide sel atoms
[Repeated 1 time(s)]
> select #3/A,C,E
7413 atoms, 7527 bonds, 3 pseudobonds, 951 residues, 2 models selected
> color sel royalblue bluie
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel royal blue
> select #3/A,C,E:ANP*,Ca*
99 atoms, 99 bonds, 9 residues, 1 model selected
> color sel royal blue
> show sel atoms
> style sel stick
Changed 99 atom styles
> select #3/B,D,F
7380 atoms, 7494 bonds, 3 pseudobonds, 948 residues, 2 models selected
> color sel wheat
> select #3/B,D,F:Ca*,ANP*
66 atoms, 66 bonds, 6 residues, 1 model selected
> show sel atoms
> select #3/M,N,O,P,Q,R,S
359 atoms, 375 bonds, 45 residues, 1 model selected
> color sel red
> show sel cartoons
> show sel atoms
> select #3/M,N,O,P,Q,R,S:18,25
Nothing selected
> select #3/M,N,O,P,Q,R,S:3,10
83 atoms, 78 bonds, 9 residues, 1 model selected
> hide sel atoms
> select #3
15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 2 models selected
> color zone #2.1 near sel distance 4.38
> transparency #2.1.1 50
> select subtract #3
Nothing selected
> show #!1 models
> hide #!1 models
> save "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
> structure RAD54B 07072025/ForAlexRAD54B.cxs"
——— End of log from Fri Jul 11 19:20:58 2025 ———
> view name session-start
opened ChimeraX session
> transparency 0.2
> transparency 0.9
> hide #!2 models
> show #!2 models
> hide #!3 models
> view p1
Expected an objects specifier or a view name or a keyword
> view name p1
> view name p2
> fly p1 p2
> fly p1 p2 p1
> save "/Users/anz/Desktop/P-motifs/2025 RAD54B paper/data/250712 CryoEM
> structures RAD54B PhePP from Sophie/ForAlexRAD54B movies TMM.cxs"
——— End of log from Wed Sep 3 19:35:27 2025 ———
> view name session-start
opened ChimeraX session
> split #4
Split 8qqe (#4) into 4 models
Chain information for 8qqe A #4.1
---
Chain | Description
A | No description available
Chain information for 8qqe B #4.2
---
Chain | Description
B | No description available
Chain information for 8qqe C #4.3
---
Chain | Description
C | No description available
Chain information for 8qqe D #4.4
---
Chain | Description
D | No description available
> split #1
Split BRCA2_m4_real_space_refined_000.pdb (#1) into 14 models
Chain information for BRCA2_m4_real_space_refined_000.pdb A #1.1
---
Chain | Description
A | No description available
Chain information for BRCA2_m4_real_space_refined_000.pdb B #1.2
---
Chain | Description
B | No description available
Chain information for BRCA2_m4_real_space_refined_000.pdb C #1.3
---
Chain | Description
C | No description available
Chain information for BRCA2_m4_real_space_refined_000.pdb D #1.4
---
Chain | Description
D | No description available
Chain information for BRCA2_m4_real_space_refined_000.pdb E #1.5
---
Chain | Description
E | No description available
Chain information for BRCA2_m4_real_space_refined_000.pdb F #1.6
---
Chain | Description
F | No description available
Chain information for BRCA2_m4_real_space_refined_000.pdb M #1.8
---
Chain | Description
M | No description available
Chain information for BRCA2_m4_real_space_refined_000.pdb N #1.9
---
Chain | Description
N | No description available
Chain information for BRCA2_m4_real_space_refined_000.pdb O #1.10
---
Chain | Description
O | No description available
Chain information for BRCA2_m4_real_space_refined_000.pdb P #1.11
---
Chain | Description
P | No description available
Chain information for BRCA2_m4_real_space_refined_000.pdb Q #1.12
---
Chain | Description
Q | No description available
Chain information for BRCA2_m4_real_space_refined_000.pdb R #1.13
---
Chain | Description
R | No description available
Chain information for BRCA2_m4_real_space_refined_000.pdb X #1.14
---
Chain | Description
X | No description available
> split #3
Split RAD54-J402_m4_real_space_refined_000.pdb (#3) into 13 models
Chain information for RAD54-J402_m4_real_space_refined_000.pdb A #3.1
---
Chain | Description
A | No description available
Chain information for RAD54-J402_m4_real_space_refined_000.pdb B #3.2
---
Chain | Description
B | No description available
Chain information for RAD54-J402_m4_real_space_refined_000.pdb C #3.3
---
Chain | Description
C | No description available
Chain information for RAD54-J402_m4_real_space_refined_000.pdb D #3.4
---
Chain | Description
D | No description available
Chain information for RAD54-J402_m4_real_space_refined_000.pdb E #3.5
---
Chain | Description
E | No description available
Chain information for RAD54-J402_m4_real_space_refined_000.pdb F #3.6
---
Chain | Description
F | No description available
Chain information for RAD54-J402_m4_real_space_refined_000.pdb M #3.7
---
Chain | Description
M | No description available
Chain information for RAD54-J402_m4_real_space_refined_000.pdb N #3.8
---
Chain | Description
N | No description available
Chain information for RAD54-J402_m4_real_space_refined_000.pdb O #3.9
---
Chain | Description
O | No description available
Chain information for RAD54-J402_m4_real_space_refined_000.pdb P #3.10
---
Chain | Description
P | No description available
Chain information for RAD54-J402_m4_real_space_refined_000.pdb Q #3.11
---
Chain | Description
Q | No description available
Chain information for RAD54-J402_m4_real_space_refined_000.pdb R #3.12
---
Chain | Description
R | No description available
Chain information for RAD54-J402_m4_real_space_refined_000.pdb X #3.13
---
Chain | Description
X | No description available
> hide #!2.1 models
> hide #!3 models
> show #!3 models
> cartoon #3
> cartoon #3.1
> view #3.1 clip false
> show #3.7-13#!3.1-6 target m
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1.1 models
> hide #!1.1 models
> show #1.11 models
> hide #1.11 models
> show #1.12 models
> hide #1.12 models
> show #1.12 models
> show #1.11 models
> hide #1.12 models
> show #1.12 models
> hide #1.12 models
> show #1.12 models
> hide #1.12 models
> hide #1.11 models
> show #1.11 models
> hide #1.11 models
> show #1.11 models
> hide #1.11 models
> show #1.11 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.2 models
> hide #!4.2 models
> show #!4.1 models
> show #!4.2 models
> hide #!4.2 models
> hide #!4.1 models
> save "/Users/anz/Desktop/P-motifs/2025 RAD54B paper/data/250712 CryoEM
> structures RAD54B PhePP from Sophie/ForAlexRAD54B movies TMM peptide 2.cxs"
> show #!1.1 models
> hide #!1.1 models
> hide #1.11 models
> show #1.11 models
> color #1.11 #941751ff
> color #1.11 #fffb00ff
> color #1.7 #fffc79ff
> show #1.7 models
> show #1.8 models
> show #1.9 models
> show #1.10 models
> color #1.10 #fffb00ff
> view #1.10 clip false
No displayed objects specified.
> select add #1.10
68 atoms, 71 bonds, 8 residues, 1 model selected
> select subtract #1.10
Nothing selected
> show #1.7-11#3.7-13#!3.1-6 atoms
> hide #1.7-11#3.7-13#!3.1-6 atoms
> show #!1.6 models
> hide #!1.6 models
> hide #!3 models
> show #!1.6 models
> show #!1.5 models
> show #!1.3 models
> show #!1.2 models
> show #!1.4 models
> show #!1.1 models
> show #!3 models
> show #!4.1 models
> show #!4.2 models
> show #4.3 models
> show #4.4 models
> hide #!1.5 models
> hide #!1 models
> show #!1 models
> style #1.7-11#3.7-13#4.3-4#!1.1-4,6#!3.1-6#!4.1-2 ball
Changed 32770 atom styles
> style #1.7-11#3.7-13#4.3-4#!1.1-4,6#!3.1-6#!4.1-2 ball
Changed 32770 atom styles
> hide #1.11 models
> show #1.11 models
> style #1.7-11#3.7-13#4.3-4#!1.1-4,6#!3.1-6#!4.1-2 ball
Changed 32770 atom styles
> show #1.7-11#3.7-13#4.3-4#!1.1-4,6#!3.1-6#!4.1-2 atoms
> hide #1.7-11#3.7-13#4.3-4#!1.1-4,6#!3.1-6#!4.1-2 atoms
> select add #1.11
68 atoms, 71 bonds, 8 residues, 1 model selected
> style sel ball
Changed 68 atom styles
> show sel atoms
> select subtract #1.11
Nothing selected
> open
> /Users/anz/Downloads/fold_rad54_nterm_rad51/fold_rad54_nterm_rad51_model_0.cif
Chain information for fold_rad54_nterm_rad51_model_0.cif #5
---
Chain | Description
A | .
B | .
Computing secondary structure
> view #5 clip false
> split #5
Split fold_rad54_nterm_rad51_model_0.cif (#5) into 2 models
Chain information for fold_rad54_nterm_rad51_model_0.cif A #5.1
---
Chain | Description
A | No description available
Chain information for fold_rad54_nterm_rad51_model_0.cif B #5.2
---
Chain | Description
B | No description available
> color #5.1 #0096ffff
> select #5.1:82
11 atoms, 11 bonds, 1 residue, 1 model selected
> show #5.1:82
> view #5 clip false
> view #4 clip false
> matchmaker #5.2 to #3.2 bring #5.1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker RAD54-J402_m4_real_space_refined_000.pdb B, chain B (#3.2) with
fold_rad54_nterm_rad51_model_0.cif B, chain B (#5.2), sequence alignment score
= 1025.4
RMSD between 260 pruned atom pairs is 0.874 angstroms; (across all 309 pairs:
1.756)
> color #5.1 #ff40ffff
> show #5.1:85
> hide #!5 models
> hide #!4.1 models
> show #!4.1 models
> mmaker #4.2 to #3.2 bring #4.1,3,4
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 RAD54-J402_m4_real_space_refined_000.pdb B, chain B (#3.2) with
8qqe B, chain B (#4.2), sequence alignment score = 1204.2
RMSD between 223 pruned atom pairs is 0.621 angstroms; (across all 247 pairs:
2.554)
> hide #!4.1 models
> hide #!4.2 models
> hide #4.4 models
> open 8pbc
8pbc title:
RAD51 filament on ssDNA bound by the BRCA2 c-terminus [more info...]
Chain information for 8pbc #6
---
Chain | Description | UniProt
A B C D E F G H I J K | DNA repair protein RAD51 homolog 1 | RAD51_HUMAN 1-339
L M N O P Q R S T U | Breast cancer type 2 susceptibility protein | BRCA2_HUMAN 3260-3308
V | DNA (30-MER) |
Non-standard residues in 8pbc #6
---
ATP — adenosine-5'-triphosphate
CA — calcium ion
> split #6
Split 8pbc (#6) into 22 models
Chain information for 8pbc A #6.1
---
Chain | Description
A | No description available
Chain information for 8pbc B #6.2
---
Chain | Description
B | No description available
Chain information for 8pbc C #6.3
---
Chain | Description
C | No description available
Chain information for 8pbc D #6.4
---
Chain | Description
D | No description available
Chain information for 8pbc E #6.5
---
Chain | Description
E | No description available
Chain information for 8pbc F #6.6
---
Chain | Description
F | No description available
Chain information for 8pbc G #6.7
---
Chain | Description
G | No description available
Chain information for 8pbc H #6.8
---
Chain | Description
H | No description available
Chain information for 8pbc I #6.9
---
Chain | Description
I | No description available
Chain information for 8pbc J #6.10
---
Chain | Description
J | No description available
Chain information for 8pbc K #6.11
---
Chain | Description
K | No description available
Chain information for 8pbc L #6.12
---
Chain | Description
L | No description available
Chain information for 8pbc M #6.13
---
Chain | Description
M | No description available
Chain information for 8pbc N #6.14
---
Chain | Description
N | No description available
Chain information for 8pbc O #6.15
---
Chain | Description
O | No description available
Chain information for 8pbc P #6.16
---
Chain | Description
P | No description available
Chain information for 8pbc Q #6.17
---
Chain | Description
Q | No description available
Chain information for 8pbc R #6.18
---
Chain | Description
R | No description available
Chain information for 8pbc S #6.19
---
Chain | Description
S | No description available
Chain information for 8pbc T #6.20
---
Chain | Description
T | No description available
Chain information for 8pbc U #6.21
---
Chain | Description
U | No description available
Chain information for 8pbc V #6.22
---
Chain | Description
V | No description available
> hide #6
> cartoon #6
> hide #!6.1 models
> hide #!6.2 models
> show #!6.1 models
> show #!6.2 models
> hide #!6.2 models
> hide #!6.1 models
> hide #!6.3 models
> hide #!6.5 models
> hide #!6.6 models
> hide #!6.7 models
> hide #!6.8 models
> hide #!6.9 models
> hide #!6.10 models
> hide #!6.11 models
> show #!6.11 models
> hide #!6.11 models
> show #!6.11 models
> mmaker #6.11 to #3.2 bring #6
Cannot 'bring' parent model of match structure
> mmaker #6.11 to #3.2 bring #6.12
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 RAD54-J402_m4_real_space_refined_000.pdb B, chain B (#3.2) with
8pbc K, chain K (#6.11), sequence alignment score = 1011.4
RMSD between 275 pruned atom pairs is 0.914 angstroms; (across all 307 pairs:
1.554)
> ~cartoon #6.11
> color #6.12 orange
> show #!6.10 models
> hide #!6.10 models
> hide #6.13 models
> show #6.13 models
> show #!6.10 models
> show #!6.9 models
> hide #6.14 models
> show #6.14 models
> hide #6.14 models
> show #6.14 models
> close #6
> open 8pbc
8pbc title:
RAD51 filament on ssDNA bound by the BRCA2 c-terminus [more info...]
Chain information for 8pbc #6
---
Chain | Description | UniProt
A B C D E F G H I J K | DNA repair protein RAD51 homolog 1 | RAD51_HUMAN 1-339
L M N O P Q R S T U | Breast cancer type 2 susceptibility protein | BRCA2_HUMAN 3260-3308
V | DNA (30-MER) |
Non-standard residues in 8pbc #6
---
ATP — adenosine-5'-triphosphate
CA — calcium ion
> hide #6
> cartoon #6
> ~cartoon #6
> cartoon #6.9,10,11,12
> split #6
Split 8pbc (#6) into 22 models
Chain information for 8pbc A #6.1
---
Chain | Description
A | No description available
Chain information for 8pbc B #6.2
---
Chain | Description
B | No description available
Chain information for 8pbc C #6.3
---
Chain | Description
C | No description available
Chain information for 8pbc D #6.4
---
Chain | Description
D | No description available
Chain information for 8pbc E #6.5
---
Chain | Description
E | No description available
Chain information for 8pbc F #6.6
---
Chain | Description
F | No description available
Chain information for 8pbc G #6.7
---
Chain | Description
G | No description available
Chain information for 8pbc H #6.8
---
Chain | Description
H | No description available
Chain information for 8pbc I #6.9
---
Chain | Description
I | No description available
Chain information for 8pbc J #6.10
---
Chain | Description
J | No description available
Chain information for 8pbc K #6.11
---
Chain | Description
K | No description available
Chain information for 8pbc L #6.12
---
Chain | Description
L | No description available
Chain information for 8pbc M #6.13
---
Chain | Description
M | No description available
Chain information for 8pbc N #6.14
---
Chain | Description
N | No description available
Chain information for 8pbc O #6.15
---
Chain | Description
O | No description available
Chain information for 8pbc P #6.16
---
Chain | Description
P | No description available
Chain information for 8pbc Q #6.17
---
Chain | Description
Q | No description available
Chain information for 8pbc R #6.18
---
Chain | Description
R | No description available
Chain information for 8pbc S #6.19
---
Chain | Description
S | No description available
Chain information for 8pbc T #6.20
---
Chain | Description
T | No description available
Chain information for 8pbc U #6.21
---
Chain | Description
U | No description available
Chain information for 8pbc V #6.22
---
Chain | Description
V | No description available
> cartoon #6.9,10,11,12
> mmaker #6.10 to #3.2 bring #6
Cannot 'bring' parent model of match structure
> mmaker #6.10 to #3.2 bring #6.9,11,12
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 RAD54-J402_m4_real_space_refined_000.pdb B, chain B (#3.2) with
8pbc J, chain J (#6.10), sequence alignment score = 1011.4
RMSD between 275 pruned atom pairs is 0.914 angstroms; (across all 307 pairs:
1.554)
> color #6.9-12 orange
> close #6
> open 8pbc
8pbc title:
RAD51 filament on ssDNA bound by the BRCA2 c-terminus [more info...]
Chain information for 8pbc #6
---
Chain | Description | UniProt
A B C D E F G H I J K | DNA repair protein RAD51 homolog 1 | RAD51_HUMAN 1-339
L M N O P Q R S T U | Breast cancer type 2 susceptibility protein | BRCA2_HUMAN 3260-3308
V | DNA (30-MER) |
Non-standard residues in 8pbc #6
---
ATP — adenosine-5'-triphosphate
CA — calcium ion
> hide #6
> split #6
Split 8pbc (#6) into 22 models
Chain information for 8pbc A #6.1
---
Chain | Description
A | No description available
Chain information for 8pbc B #6.2
---
Chain | Description
B | No description available
Chain information for 8pbc C #6.3
---
Chain | Description
C | No description available
Chain information for 8pbc D #6.4
---
Chain | Description
D | No description available
Chain information for 8pbc E #6.5
---
Chain | Description
E | No description available
Chain information for 8pbc F #6.6
---
Chain | Description
F | No description available
Chain information for 8pbc G #6.7
---
Chain | Description
G | No description available
Chain information for 8pbc H #6.8
---
Chain | Description
H | No description available
Chain information for 8pbc I #6.9
---
Chain | Description
I | No description available
Chain information for 8pbc J #6.10
---
Chain | Description
J | No description available
Chain information for 8pbc K #6.11
---
Chain | Description
K | No description available
Chain information for 8pbc L #6.12
---
Chain | Description
L | No description available
Chain information for 8pbc M #6.13
---
Chain | Description
M | No description available
Chain information for 8pbc N #6.14
---
Chain | Description
N | No description available
Chain information for 8pbc O #6.15
---
Chain | Description
O | No description available
Chain information for 8pbc P #6.16
---
Chain | Description
P | No description available
Chain information for 8pbc Q #6.17
---
Chain | Description
Q | No description available
Chain information for 8pbc R #6.18
---
Chain | Description
R | No description available
Chain information for 8pbc S #6.19
---
Chain | Description
S | No description available
Chain information for 8pbc T #6.20
---
Chain | Description
T | No description available
Chain information for 8pbc U #6.21
---
Chain | Description
U | No description available
Chain information for 8pbc V #6.22
---
Chain | Description
V | No description available
> color #6 orange
> cartoon #6
> ~cartoon #6
> cartoon #6.10-13
> mmaker #6.11 to #3.2 bring #6.10,12,13
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 RAD54-J402_m4_real_space_refined_000.pdb B, chain B (#3.2) with
8pbc K, chain K (#6.11), sequence alignment score = 1011.4
RMSD between 275 pruned atom pairs is 0.914 angstroms; (across all 307 pairs:
1.554)
> ~cartoon #6
> show #6.13
> hide #6.13
> hide #6.12
> show #6.12 stick
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show #6.12 atoms
> select #6.12
121 atoms, 125 bonds, 16 residues, 1 model selected
> style sel ball
Changed 121 atom styles
> ~select
Nothing selected
> name peptides #6.12 | #3.8 | #1.11 | #4.3
> style peptides sticks
Expected a keyword
> style peptides stick
Changed 355 atom styles
> style peptides ball
Changed 355 atom styles
> show peptides
> name apple #6.10-13
> cartoon apple
> log metadata #6.12
The model has no metadata
> log chains #6.12
Chain information for 8pbc L #6.12
---
Chain | Description
L | No description available
> select #6.12/L:3289-3304
121 atoms, 125 bonds, 16 residues, 1 model selected
> sequence chain #6.12/L
Alignment identifier is 6.12/L
> select #6.12/L:3298
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #6.12/L:3298-3301
34 atoms, 36 bonds, 4 residues, 1 model selected
> color #6.12 lightGrey
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #6.12 azure
> color #6.12 byatom
> select up
121 atoms, 125 bonds, 16 residues, 1 model selected
> color #6.12 azure
> color #6.12 byhetero
> ~cartoon #6.10,11,13
> ~select
Nothing selected
> surface #3.2
> surface #3.2 transparency 80
> surface #3.2 transparency 30
> show #3.3:89
> color #3.3:89 byhetero
> select #6.12/L:3289
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #6.12/L
121 atoms, 125 bonds, 16 residues, 1 model selected
> select #6.12/L:3298
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #6.12/L:3298-3301
34 atoms, 36 bonds, 4 residues, 1 model selected
> hide #6.12 & ! :3298-3301
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide (#6.12 & ! :3298-3301)
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide (#6.12 & ! :3298-3301) atoms
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #6.12 & ~:3298-3301 atoms
> ~cartoon #6.12
> select ~sel & ##selected
87 atoms, 89 bonds, 12 residues, 1 model selected
> ~cartoon #1.11
> ~cartoon #3.8
> ~cartoon #4.3
> save "/Users/anz/Desktop/P-motifs/2025 RAD54B paper/data/250712 CryoEM
> structures RAD54B PhePP from Sophie/ForAlexRAD54B movies TMM peptide 2.cxs"
> hide #6.12 models
> select add #6.12
121 atoms, 125 bonds, 16 residues, 1 model selected
> select subtract #6.12
Nothing selected
> show #6.12 models
> hide #6.12 models
> show #6.12 models
> hide #6.12 models
> color #4.3 thistle
> view #4.4 clip false
No displayed objects specified.
> view #4.3 clip false
> color #4.3 byhetero
> name FPP #6.12:3298,3230,3231 | #3.8:5,7,8 | #1.11:5,7,8 | #4.3:2406,2408,2409
> select FPP
86 atoms, 89 bonds, 10 residues, 4 models selected
> name list
ANP #3:ANP
FPP #6.12:3298,3230,3231 | #3.8:5,7,8 | #1.11:5,7,8 | #4.3:2406,2408,2409
R54B #3/M-R
apple #6.10-13
peptides #6.12 | #3.8 | #1.11 | #4.3
phe85 #3:85
> hide peptides
> show FPP
> view name core1
> select ~sel & ##selected
269 atoms, 279 bonds, 35 residues, 4 models selected
> view name core2
> view name core3
> view core1
> move record
Missing or invalid "axis" argument: Expected 3 floats or "x", or "y", or "z"
or two atoms
> movie record
> fly core1 core2 core3 core1
> movie encode FPP.mp4
Movie saved to FPP.mp4
> movie encode /Users/anz/Desktop/FPP.mp4
No frames have been recorded
> select up
283 atoms, 279 bonds, 45 residues, 4 models selected
> select up
355 atoms, 368 bonds, 45 residues, 4 models selected
> select up
4630 atoms, 4711 bonds, 596 residues, 7 models selected
> select up
20410 atoms, 20483 bonds, 2840 residues, 20 models selected
> select up
35858 atoms, 36207 bonds, 4794 residues, 32 models selected
> select down
20410 atoms, 20483 bonds, 2840 residues, 21 models selected
> select down
4630 atoms, 4711 bonds, 596 residues, 7 models selected
> select down
355 atoms, 368 bonds, 45 residues, 4 models selected
> select down
283 atoms, 279 bonds, 45 residues, 4 models selected
> select down
269 atoms, 279 bonds, 35 residues, 4 models selected
> movie record
> fly core1 core2 core3 core1
> save "/Users/anz/Desktop/P-motifs/2025 RAD54B paper/data/250712 CryoEM
> structures RAD54B PhePP from Sophie/ForAlexRAD54B movies TMM peptide 2.cxs"
> ~cartoon #3.1,4,5,6
> ~cartoon #3.7,9-12
> select ~sel & ##selected
86 atoms, 89 bonds, 10 residues, 4 models selected
> ~cartoon #3.7,9-13
> hide FPP
> show #3.8 | #1.11
> color #3.8 coral
> hide #3.8
> hide #1.11
> crossfade
> show #3.8
> movie stop
> movie reset
> ~select
Nothing selected
> color #3.8 byhetero
> lighting full
> lighting soft
> lighting simple
> lighting full
> lighting simple
> lighting soft
> lighting full
> color #1.11 byhetero
> view name cryo1
> select ~sel & ##selected
Nothing selected
> view name cryo2
> select ~sel & ##selected
Nothing selected
> view name cryo3
> view name cryo4
> view cryo1
> movie record
> fly cryo1 cryo2 cryo3 cryo4 cryo1
> crossfade
> show #1.11
> wait 20
> fly cryo1 30 cryo2
> fly cryo2 30 cryo3 30 cryo4 30 cryo1
> movie encode cryo.mp4
Movie saved to cryo.mp4
> movie record
> crossfade
> hide peptides & ~FPP
> crossfade
> show FPP
> fly cryo1 20 cryo2 40 cryo3 30 cryo4 10 cryo1
> movie encode FPP2.mp4
Movie saved to FPP2.mp4
> view core1
> view name core2
> select ~sel & ##selected
Nothing selected
> view name core3
> hide FPP
> show #3.8
> view core1
> movie record
> fly core1 core2 core3 core1
> crossfade
> show #1.11
> fly core1 core2 core1
> movie stop
> movie reset
> view core1
> hide #1.11
> movie record
> fly core1 core2 core3 core1
> crossfade
> show #1.11
> fly core1 30 core2
> fly core2 20 core3 20 core1
> movie encode cryo.mp4
Movie saved to cryo.mp4
> view core1
> hide peptides
> movie record
> crossfade 10
> show #3.8
> wait 10
> crossfade 20
> show #1.1
> hide #1.1
> resest
Unknown command: movie resest
> movie stop
> movie reset
> hide peptides
> movie record
> crossfade 10
> show #3.8
> wait 10
> crossfade 20
> show #1.11
> fly core1 core2 core3 core1
> movie encode cryo.mp4
Movie saved to cryo.mp4
> view core1
> movie record
> crossfade 10
> show #4.3
> crossfade 10
> show #6.12
> show #6.12 models
> crossfade 10
> show #6.12
> crossfade 10
> hide peptids & ~FPP
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> crossfade 10
> hide peptides & ~FPP
> fly core1 core2 core3 core1
> movie encode FPP.mp4
Movie saved to FPP.mp4
> hide peptides
> show #3.8 | #1.11
> movie record
> crossfade 20
> show #4.3
> wait 10
> crossfade 20
> show #6.12
> wait 15
> crossfade 20
> hide peptides & ~FPP
> fly core1 core2
> fly core2 core3 core1
> movie encode FPP.mp4
Movie saved to FPP.mp4
> hide FPP
> show #3.8 | #1.11
> movie record
> crossfade 40
> show #6.2
> movie stop
> movie reset
> hide #6.2
> movie record
> crossfade 40
> show #6.12
> movie stop
> movie reset
> movie record
> movie stop
> hide #6.12
> movie record
> crossfade 40
> show #4.3
> crossfade 40
> show #6.12
> wait 20
> crossfade 30
> hide peptides & ~FPP
> fly core1 core2 core3 core1
> movie encode FPP2.mp4
Movie saved to FPP2.mp4
> hide FPP
> show #1.11
> hide #1.11
> show #3.8
> view name r54b1
> select ~sel & ##selected
Nothing selected
> view name r54b2
> view name r54b3
> view r54b1
> movie record
> fly r54b1 r54b2 r54b3 r54b4
fly: Unknown position name "r54b4"
> fly r54b1 r54b2 r54b3 r54b1
> movie encode r54b.mp4
Movie saved to r54b.mp4
> movie record
> crossfade 30
> coulombic #3.2
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for RAD54-J402_m4_real_space_refined_000.pdb B_B SES surface
#3.2.2: minimum, -19.17, mean -0.61, maximum 13.24
> movie encode r54b-es.mp4
Movie saved to r54b-es.mp4
> view r54b1
> ~surface #3.2
> surface #3.2
> hide #3.8
> show #1.11
> movie record
> fly r54b1 r54b3
> crossfade 40
> show #4.3
> movie stop
> view name phepp1
> view r54b3
> movie record
> fly r54b3 phepp1
> wait 30
> fly phepp1 r54b1
> movie encode phepp.mp4
Movie saved to phepp.mp4
> save "/Users/anz/Desktop/P-motifs/2025 RAD54B paper/data/250712 CryoEM
> structures RAD54B PhePP from Sophie/ForAlexRAD54B movies TMM peptide 2.cxs"
——— End of log from Thu Sep 4 04:53:36 2025 ———
> view name session-start
opened ChimeraX session
> label listfonts
221 fonts available:
.Apple Symbols Fallback
.AppleSystemUIFont
.Times Fallback
Academy Engraved LET
Al Bayan
Al Nile
Al Tarikh
Aller
Aller Display
American Typewriter
Andale Mono
Apple Braille
Apple Chancery
Apple Color Emoji
Apple SD Gothic Neo
Apple Symbols
AppleGothic
AppleMyungjo
Aptos
Aptos Mono
Aptos Narrow
Aptos Serif
Arial
Arial Black
Arial Hebrew
Arial Hebrew Scholar
Arial Narrow
Arial Rounded MT Bold
Arial Unicode MS
Avenir
Avenir Next
Avenir Next Condensed
Ayuthaya
Baghdad
Bahnschrift
Bangla MN
Bangla Sangam MN
Baskerville
Beirut
Big Caslon
Bodoni 72
Bodoni 72 Oldstyle
Bodoni 72 Smallcaps
Bodoni Ornaments
Bradley Hand
Braggadocio
Brush Script MT
Canela Text
Chalkboard
Chalkboard SE
Chalkduster
Charter
Cochin
Comic Sans MS
Consolas
Copperplate
Corsiva Hebrew
Courier New
DIN Alternate
DIN Condensed
Damascus
Darkwoman
DecoType Naskh
Devanagari MT
Devanagari Sangam MN
Didot
Diwan Kufi
Diwan Thuluth
Euphemia UCAS
Farah
Farisi
Futura
GB18030 Bitmap
Galvji
Geeza Pro
Geneva
Georgia
Gill Sans
Gloucester MT Extra Condensed
Grantha Sangam MN
Gujarati MT
Gujarati Sangam MN
Gurmukhi MN
Gurmukhi MT
Gurmukhi Sangam MN
Heiti SC
Heiti TC
Helvetica
Helvetica Neue
Herculanum
Hiragino Maru Gothic ProN
Hiragino Mincho ProN
Hiragino Sans
Hiragino Sans GB
Hobo Std
Hoefler Text
ITF Devanagari
ITF Devanagari Marathi
Impact
InaiMathi
Kailasa
Kannada MN
Kannada Sangam MN
Kefa III
Khmer MN
Khmer Sangam MN
Kohinoor Bangla
Kohinoor Devanagari
Kohinoor Gujarati
Kohinoor Telugu
Kokonor
Kotyhoroshko
Koziyar
Krungthep
KufiStandardGK
KurkaLapoyu
Lao MN
Lao Sangam MN
LevType Hryvnia
Lucida Blackletter
Lucida Grande
Lugatype
Luminari
Malayalam MN
Malayalam Sangam MN
Marker Felt
Matura MT Script Capitals
Menlo
Microsoft Sans Serif
Mishafi
Mishafi Gold
Monaco
Montserrat
Mshtakan
Mukta Mahee
Muna
Myanmar MN
Myanmar Sangam MN
Nadeem
New Peninim MT
Noteworthy
Noto Emoji
Noto Nastaliq Urdu
Noto Sans
Noto Sans Armenian
Noto Sans Batak
Noto Sans Condensed
Noto Sans ExtraCondensed
Noto Sans Kannada
Noto Sans Myanmar
Noto Sans NKo
Noto Sans Oriya
Noto Sans SemiCondensed
Noto Sans Syriac
Noto Sans Tagalog
Noto Sans Zawgyi
Noto Serif Myanmar
Open Sans
Open Sans Condensed
Open Sans SemiCondensed
Optima
Oriya MN
Oriya Sangam MN
PT Mono
PT Sans
PT Sans Caption
PT Sans Narrow
PT Serif
PT Serif Caption
Palatino
Papyrus
Party LET
Phosphate
PingFang HK
PingFang MO
PingFang SC
PingFang TC
Plantagenet Cherokee
Proxima Nova
Publico Text
Raanana
Roboto
Roboto Condensed
Roboto SemiCondensed
Rockwell
STIX Two Math
STIX Two Text
STSong
Sana
Sathu
Savoye LET
Segoe UI
Shree Devanagari 714
SignPainter
Silom
Sinhala MN
Sinhala Sangam MN
Skia
Snell Roundhand
Songti SC
Songti TC
Sukhumvit Set
Symbol
Tahoma
Tamil MN
Tamil Sangam MN
Telugu MN
Telugu Sangam MN
Thonburi
Times New Roman
Trattatello
Trebuchet MS
Veles
Verdana
Waseem
Webdings
Wingdings
Wingdings 2
Wingdings 3
Zapf Dingbats
Zapfino
> label #3.2/B:182
> label #3.2/B:182,180
> label #3.2/B:182 hight 5
Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword
> label #3.2/B:182 residues hight 5
Expected a keyword
> label #3.2/B:182 residues height 5
> label #3.2/B:182 residues height 2
> label #3.2/B:182 residues height 1
> label #3.2/B:172,175,180,182,186 residues height 1
> label #3.2/B:172,175,180,182,186 residues height 1 font "Aller Display"
> label #3.2/B:172,175,180,182,186 residues height 1.5 font "Aller Display"
> label #3.2/B:168,172,175,180,182,186 residues height 1.5 font "Aller
> Display"
> log metadata #3.10
The model has no metadata
> log chains #3.10
Chain information for RAD54-J402_m4_real_space_refined_000.pdb P #3.10
---
Chain | Description
P | No description available
> ui tool show "Renumber Residues"
> show #3.10 target m
> ui tool show "Show Sequence Viewer"
> sequence chain #6.12/L #6.13/M #6.14/N #6.15/O #6.16/P #6.17/Q #6.18/R
> #6.19/S #6.20/T #6.21/U
Alignment identifier is 1
> pwd
Current working directory is: /Users/anz/Desktop
> save 251009_lysines
Cannot determine format for '251009_lysines'
> save 251009_lysines.csx
No known data format for file suffix '.csx'
> save 251009_lysines.cxs
> cartoon #3.2
> select ~sel & ##selected
Nothing selected
> cartoon #3.1
> select add #3.1
2471 atoms, 2509 bonds, 1 pseudobond, 317 residues, 2 models selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for RAD54-J402_m4_real_space_refined_000.pdb A_A SES surface
#3.1.2: minimum, -27.47, mean -0.69, maximum 13.40
To also show corresponding color key, enter the above coulombic command and
add key true
> ui tool show "Show Sequence Viewer"
> sequence chain #3.8/N #3.9/O #3.10/P #3.11/Q
Alignment identifier is 1
> ui tool show "Renumber Residues"
> hide #1
> select ~sel & ##selected
Nothing selected
> hide #4
> show #3.4
> hide #3.4
> show #3.10
> select ~sel & ##selected
Nothing selected
> hide #3.10
> show #!4.2 models
> hide #!4.2 models
> show #4
> select ~sel & ##selected
Nothing selected
> hide #4
Cell requested for row 12 is out of bounds for table with 26 rows! Resizing
table model.
> show #3.2
> hide #3.2
> show #3.8,9,10,11
> save 251009_lysines.cxs
——— End of log from Thu Oct 9 14:13:54 2025 ———
> view name session-start
opened ChimeraX session
> surface #3.2 transparency 80
> surface #3.2 transparency 60
> select #3.3:57,57,255
20 atoms, 18 bonds, 2 residues, 1 model selected
> style sel ball
Changed 20 atom styles
> show sel atoms
> select #3.3:56,57,255
31 atoms, 29 bonds, 3 residues, 1 model selected
> show sel atoms
> select #3.3:56,57,255,252
42 atoms, 39 bonds, 4 residues, 1 model selected
> show sel atoms
> select ~sel & ##selected
2429 atoms, 2470 bonds, 1 pseudobond, 313 residues, 2 models selected
> select ~sel & ##selected
42 atoms, 39 bonds, 4 residues, 1 model selected
> label #3.2:197,201,204,238
> select ~sel & ##selected
2429 atoms, 2470 bonds, 1 pseudobond, 313 residues, 2 models selected
> label #3.2:197,201,204,238 residues height 1.5 font "Aller Display"
> label #3.2:197,201,204,238,232,238,241 residues height 1.5 font "Aller
> Display"
> ~label #3.2:197,201,204,238,232,238,241 residues height 1.5 font "Aller
> Display"
> label delete #3.2:197,201,204,238,232,238,241 residues height 1.5 font
> "Aller Display"
Expected a keyword
> ~label #3.2:197,201,204,238,232,238,241
> label #3.2:197,201,204,238 residues height 1.5 font "Aller Display"
> label #3.1:232,238,241 residues height 1.5 font "Aller Display"
> save 251009_lysines.cxs
> select up
2435 atoms, 2470 bonds, 1 pseudobond, 317 residues, 2 models selected
> select add #3
15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 22 models selected
> select subtract #3
2 models selected
> ui tool show "Renumber Residues"
> renumber #3.8/N #3.9/O #3.10/P #3.11/Q seqStart 18
32 residues renumbered
> hide #3.10,11
> hide #3.9-11
> save 251009_lysines.cxs
> lighting shadows false
> lighting shadows true
> lighting shadows false
> select #3.1
2471 atoms, 2509 bonds, 1 pseudobond, 317 residues, 3 models selected
> mlp sel
Map values for surface "RAD54-J402_m4_real_space_refined_000.pdb A_A SES
surface": minimum -28.84, mean -5.01, maximum 21.74
To also show corresponding color key, enter the above mlp command and add key
true
> save 251009_lysines.cxs
——— End of log from Thu Oct 9 18:29:50 2025 ———
> view name session-start
opened ChimeraX session
> surface #3.2 transparency 10
> label #3.2:23,212
> label #3.2:23,212 residues height 1.5 font "Aller Display"
> label #3.2:23,212,213 residues height 1.5 font "Aller Display"
> save /Users/anz/Desktop/251009_lysines.cxs
> select #3.2:212,213,23
26 atoms, 24 bonds, 3 residues, 1 model selected
> show sel atoms
> surface #3.2 transparency 90
Alignment identifier is 3.2/B
> select
> #3.2/B:24-30,34-43,48-53,56-61,67-80,88-97,106-112,132-144,167-176,181-187,196-212,227-232,236-260,290-296
1179 atoms, 1180 bonds, 145 residues, 1 model selected
> select
> #3.2/B:121-126,155-160,188-192,217-223,263-268,270-272,285-287,299-305,310-317,325-331,334-337
494 atoms, 491 bonds, 62 residues, 1 model selected
> select #3.2/B:23
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.2/B:23-25
24 atoms, 23 bonds, 3 residues, 1 model selected
> select
> #3.2/B:24-30,34-43,48-53,56-61,67-80,88-97,106-112,132-144,167-176,181-187,196-212,227-232,236-260,290-296
1179 atoms, 1180 bonds, 145 residues, 1 model selected
> select #3.2/B:23-25
24 atoms, 23 bonds, 3 residues, 1 model selected
> select #3.2:25
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> label #3.2:23,25,212,213 residues height 1.5 font "Aller Display"
> select up
60 atoms, 60 bonds, 7 residues, 2 models selected
> select up
2013 atoms, 2044 bonds, 257 residues, 2 models selected
> select down
60 atoms, 60 bonds, 7 residues, 2 models selected
> select down
8 atoms, 7 bonds, 1 residue, 2 models selected
> select down
8 atoms, 7 bonds, 1 residue, 2 models selected
> surface #3.2 transparency 30
> save /Users/anz/Desktop/251009_lysines.cxs
——— End of log from Mon Oct 13 17:24:42 2025 ———
> view name session-start
opened ChimeraX session
> pwd
Current working directory is: /Users/anz/Desktop/P-motifs/2025 RAD54B
paper/2025 experiments/250915 AF Models DMC1 RAD54B
> open "/Users/anz/Desktop/P-motifs/2025 RAD54B paper/2025 experiments/250915
> AF Models DMC1 RAD54B/all_AF_models.cif"
Summary of feedback from opening /Users/anz/Desktop/P-motifs/2025 RAD54B
paper/2025 experiments/250915 AF Models DMC1 RAD54B/all_AF_models.cif
---
warnings | Unknown polymer entity '1' on line 116
Unknown polymer entity '2' on line 1396
Missing or incorrect sequence information. Inferred polymer connectivity.
Chain information for all_AF_models.cif #7
---
Chain | Description
A B C D E | No description available
F G | No description available
> split #7
Split all_AF_models.cif (#7) into 7 models
Chain information for all_AF_models.cif A #7.1
---
Chain | Description
A | No description available
Chain information for all_AF_models.cif B #7.2
---
Chain | Description
B | No description available
Chain information for all_AF_models.cif C #7.3
---
Chain | Description
C | No description available
Chain information for all_AF_models.cif D #7.4
---
Chain | Description
D | No description available
Chain information for all_AF_models.cif E #7.5
---
Chain | Description
E | No description available
Chain information for all_AF_models.cif F #7.6
---
Chain | Description
F | No description available
Chain information for all_AF_models.cif G #7.7
---
Chain | Description
G | No description available
> view #7
> cartoon #7
> hide #7
> delete #2
[Repeated 1 time(s)]
Cell requested for row 1 is out of bounds for table with 33 rows! Resizing
table model.
> close #2
> hide #7.1 models
> show #7.1 models
> select add #7
6582 atoms, 6695 bonds, 846 residues, 9 models selected
> color sel bychain
> select subtract #7
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #7.1
264 atoms, 269 bonds, 34 residues, 2 models selected
> select subtract #7.1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #3.2
2471 atoms, 2509 bonds, 1 pseudobond, 317 residues, 5 models selected
> view #3
> mmaker #7.7 to #3.2 bring #7.1-6
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 RAD54-J402_m4_real_space_refined_000.pdb B, chain B (#3.2) with
all_AF_models.cif G, chain G (#7.7), sequence alignment score = 1569
RMSD between 312 pruned atom pairs is 0.526 angstroms; (across all 314 pairs:
0.761)
> select
74534 atoms, 75562 bonds, 93 pseudobonds, 9756 residues, 111 models selected
> ~select
Nothing selected
> ~cartoon #7.4
Unsupported scale factor (0.000000) detected on Display1
[Repeated 2 time(s)]
> save "/Users/anz/Desktop/P-motifs/2025 RAD54B paper/2025
> experiments/251020_lysines.cxs"
> select #7.6:1-20
160 atoms, 161 bonds, 20 residues, 1 model selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for all_AF_models.cif F_F SES surface #7.6.1: minimum,
-19.36, mean -2.31, maximum 14.11
To also show corresponding color key, enter the above coulombic command and
add key true
> select #7.:1-20
Expected an objects specifier or a keyword
> select #7.7:1-20
160 atoms, 161 bonds, 20 residues, 1 model selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for all_AF_models.cif G_G SES surface #7.7.1: minimum,
-22.31, mean -2.76, maximum 12.63
To also show corresponding color key, enter the above coulombic command and
add key true
> ~select
Nothing selected
> rename #7.6 "DMC1 in model 1"
> rename #7.7 "DMC1 in model 4"
> rename #7.6 "DMC1 in model 0"
> rename #7.1 "54B model 0"
> rename #7.2 "54B model 1"
> rename #7.3 "54B model 2"
> rename #7.4 "54B model 3"
> rename #7.5 "54B model 4"
Alignment identifier is 4.1/A
Alignment identifier is 4.2/B
Alignment identifier is 4.3/C
Alignment identifier is 4.4/D
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
Alignment identifier is 3.7/M
Alignment identifier is 4
Alignment identifier is 3.12/R
Alignment identifier is 5.1/A
Alignment identifier is 5.2/B
Alignment identifier is 5
Alignment identifier is 6
Alignment identifier is 6.22/V
Alignment identifier is 7
Alignment identifier is 8
>
Unknown command: sequence #7.7
>
Incomplete command: sequence
> select #7.7
2647 atoms, 2689 bonds, 340 residues, 1 model selected
Alignment identifier is 7.7/G
> ~select #7.7
1 model selected
> select #7.7/G:3
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7.7/G:3-4
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #7.7/G:9
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7.7/G:9-10
18 atoms, 17 bonds, 2 residues, 1 model selected
> select #7.7/G:15
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #7.7/G:15-18
35 atoms, 34 bonds, 4 residues, 1 model selected
> label #7.6-7:3,4,9,10,15-18 residues height 1.5 font "Aller Display"
> save "/Users/anz/Desktop/P-motifs/2025 RAD54B paper/2025
> experiments/251020_lysines.cxs"
——— End of log from Tue Oct 21 09:05:15 2025 ———
> view name session-start
opened ChimeraX session
> ~label #3.2
> surface #7.7/1-18 transparency 90
No atoms specified by #7.7/1-18
> surface #7.7:1-18 transparency 90
> surface #7.6:1-18 transparency 90
> transparency #7.6:1-18 90 cartoons
> transparency #7.6:1-18 70 cartoons
> transparency #7.6:1-18 50 cartoons
> transparency #7.6:1-18 10 cartoons
> transparency #7.6:1-18 0.2 cartoons
> transparency #7.6:1-18 1 cartoons
> transparency #7.6:1-18 15 cartoons
> transparency #7.6:1-18 10 cartoons
> transparency #7.6:1-18 1 cartoons
> transparency #7.6:1-18 2 cartoons
> transparency #7.6:1-18 0.2 cartoons
> transparency #7.6:1-18 0.3 cartoons
> transparency #7.6:1-18 50 cartoons
> select up
80 atoms, 81 bonds, 10 residues, 1 model selected
> select up
2647 atoms, 2689 bonds, 340 residues, 2 models selected
> select up
2647 atoms, 2689 bonds, 340 residues, 3 models selected
> surface #7.7:1-18 transparency 80
> surface #7.6,7:1-18 transparency 80
> surface #7.6,7:1-18 transparency 86
> ~select
Nothing selected
> hide #!7.7 models
> show #!7.7 models
> hide #!7.7 models
> show #!7.7 models
> transparency #7.6:1-18 50 cartoons
> hide #!7.7 models
> show #!7.7 models
> transparency #7.6:1-18 50 ccartoons
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency #7.6:1-18 50 cartoons
> transparency #7.7:1-18 50 cartoons
> coulombic #3.1
Coulombic values for RAD54-J402_m4_real_space_refined_000.pdb A_A SES surface
#3.1.2: minimum, -27.47, mean -0.69, maximum 13.40
> transparency #3.1 80 surfaces
> transparency #3.1 80 cartoons
> transparency #3.1 79 cartoons
> transparency #3.1 81 cartoons
> lighting soft
> lighting simple
> lighting soft
> lighting full
> ~cartoon #7
> cartoon #7.1-5
> lighting soft
> transparency #3.3 90 cartoons
> select ~sel & ##selected
Nothing selected
> pwd
Current working directory is: /Users/anz/Desktop
> save 260127_lysines.cxs
> select #7.1-5:LYS,ARG
300 atoms, 280 bonds, 30 residues, 5 models selected
> style sel ball
Changed 300 atom styles
> style sel ball
Changed 300 atom styles
> show sel atoms
> color sel byhetero
> transparency #7.1-5 60 cartoons
> ~select
Nothing selected
> hide #7.1-5 atoms
> hide #7.7 atoms
> hide #3.8 atoms
> show #7.1-5:LYS,ARG atoms
> select ~sel & ##selected
Nothing selected
> color #7.1-5:LYS,ARG blue
> hide #3 atoms
> hide #3.2 cartoons
[Repeated 1 time(s)]
> hide #3.2 cartoonsd
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #3.2 cartoons
> hide #7.6-7 cartoons
> hide #3.2 cartoons
> hide #3.2
> hide #!3.2 models
> show #!3.2 models
> hide #4.3 models
> show #4.3 models
> hide #3.2.2 models
> show #3.2.2 models
> select ~sel & ##selected
Nothing selected
> hide #1.4
> hide #1.4 cartoons
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting flat
> graphics silhouettes false
> lighting full
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows false
> lighting shadows true
> lighting flat
> lighting full
> lighting soft
> save 260127_lysines.cxs
> hide #!7 models
> ~label #3.1
> ~surface #3.1,2
> cartoon 3.2
Expected an atoms specifier or a keyword
> show #3.2 cartoons
> show #3.8 cartoons
> color #3.8 red
> save view1.png
[Repeated 1 time(s)]
> show #7.6,7:1-19 cartoons
> show #7.6:1-19 cartoons
> hide #!7.6 models
> show #!7.6 models
> hide #!7.7 models
> show #!7.7 models
> hide #!7.7 models
> hide #!7.6 models
> hide #!7 models
> show #7.6:1-19 cartoons transparency 0
Expected ',' or a keyword
> transparency #7.6,7:1-19 0 cartoons
> show #7.6:1-19 cartoons
> show #7.6 cartoons
> show #!7 models
> show #!7.7 models
> show #!7.6 models
> hide #7.6,7 cartoons
> hide #7.6,7 surfaces
> hide #7.1-5 surfaces
> hide #7.1-5
> hide #7.1-5 cartoons
> show #7.1-5 cartoons
> select ~sel & ##selected
Nothing selected
> show #3.2 surfaces
> label #3.2/B:213 residues height 1.5 font "Aller Display"
> hide #7.4
> hide #7.4 cartoons
> select zone #7.5:2 5 #3.1
Nothing selected
> select zone #7.5:2 8 #3.1
Nothing selected
> select zone #7.5:2 8 #3.1
Nothing selected
> distance #7.5:2 #3.1:234
Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 17 atoms and 0
measurable objects
> save 260127_lysines.cxs
> label #3.2/B:201,204,212,213 residues height 1.5 font "Aller Display"
> show #3.2/B:201,204,212,213 atoms
> ~surface #3.2
> surface #7.6:1-18
> select ~sel & ##selected
Nothing selected
> ~surface #7.6:1-18
> surface #7.7:1-18
> surface #7.7:1-18 transparency 50
> save 260127_lysines.cxs
> ~label
> label
> show #3.2/B:201,204,212,213,238 atoms
> label #3.2/B:201,204,212,213,238 residues height 1.5 font "Aller Display"
> label #3.2/B:201,204,212,213 OR #3.1:238 residues height 1.5 font "Aller
> Display"
Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword
> label #3.2/B:201,204,212,213 | #3.1:238 residues height 1.5 font "Aller Display"
> cd "/Users/anz/Desktop/P-motifs/2025 RAD54B paper/2025 experiments/XX25-36
> GST pull-down DMC1 mutants negatively charged"
Current working directory is: /Users/anz/Desktop/P-motifs/2025 RAD54B
paper/2025 experiments/XX25-36 GST pull-down DMC1 mutants negatively charged
> save 260127_lysines_XX25-36.cxs
> save "260127 54B positive and DMC1 negative residues tested in XX25-36.cxs"
——— End of log from Wed Jan 28 15:35:48 2026 ———
> view name session-start
opened ChimeraX session
> rename #4 "8qqe our DMC1 Xray"
> hide #5.1 models
> show #5.1 models
> hide #5.1 models
> show #5.1 models
> rename #5 "RAD54 on RAD51 2025.cif"
> rename #5.1 RAD51
> rename #5.2 "RAD54 1-118"
> rename #5.2 "RAD54 1-150"
> rename #1 "DMC1-PhePP Cryo.pdb"
> rename #3 "DMC1-RAD54 Cryo"
> rename #1 "DMC1-PhePP Cryo"
> rename #5 "RAD54 on RAD51 2025 AF_0"
> rename #7 "54B on DMC1 AF models"
> rename #6 "8pbc TR2 RAD51 Cryo"
> hide #!1 models
> rename #1 "PhePP DMC1 Cryo"
> rename #3 "RAD54B DMC1 Cryo"
> rename #4 "PhePP DMC1 Xray 8qqe"
> rename #6 "TR2 RAD51 Cryo 8pbc "
> rename #7 "RAD54B on DMC1 AF models"
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7.7 models
> hide #!7.6 models
> show #!7.6 models
> hide #!7.6 models
> hide #7.5 models
> show #7.5 models
> hide #5.2 models
> show #5.2 models
> hide #5.2 models
> show #5.2 models
> hide #5.2 models
> show #5.2 models
> hide #5.1 models
> show #5.1 models
> rename #5.1 "RAD54 1-150"
> rename #5.2 RAD51
> hide #5.2 models
> select add #5.1
1187 atoms, 1216 bonds, 150 residues, 1 model selected
> color bfactor sel
1187 atoms, 150 residues, atom bfactor range 21.3 to 96.6
> save "/Users/anz/Desktop/P-motifs 260222.cxs"
——— End of log from Sat Feb 21 18:41:51 2026 ———
> view name session-start
opened ChimeraX session
> rename #3.13 DNA
> rename #3.7 "54B peptide 1"
> rename #3.8 "54B peptide 2"
> rename #3.9 "54B peptide 3"
> rename #3.10 "54B peptide 4"
> rename #3.11 "54B peptide 5"
> rename #3.12 "54B peptide 6"
> rename #3.1 DMC1
> rename #3.2 DMC1
> rename #3.3 DMC1
> rename #3.5-6 DMC1
> rename #3.4-6 DMC1
> save "/Users/anz/Desktop/P-motifs 260222.cxs"
[Repeated 1 time(s)]
> open 9QNC
Summary of feedback from opening 9QNC fetched from pdb
---
notes | Fetching compressed mmCIF 9qnc from http://files.rcsb.org/download/9qnc.cif
Fetching CCD MG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif
9qnc title:
RAD51 filament in complex with magnesium and ATP bound by the RAD51AP1
C-terminus [more info...]
Chain information for 9qnc #2
---
Chain | Description | UniProt
A C E G I K | DNA repair protein RAD51 homolog 1 | RAD51_HUMAN 1-339
B D F H J L | RAD51-associated protein 1 | R51A1_HUMAN 328-352
Z | DNA |
Non-standard residues in 9qnc #2
---
ATP — adenosine-5'-triphosphate
K — potassium ion
MG — magnesium ion
> split #8
> rename #2 "AP1 RAD51 XZ 9qnc"
> hide
> split #2
Split AP1 RAD51 XZ 9qnc (#2) into 13 models
Chain information for AP1 RAD51 XZ 9qnc A #2.1
---
Chain | Description
A | No description available
Chain information for AP1 RAD51 XZ 9qnc B #2.2
---
Chain | Description
B | No description available
Chain information for AP1 RAD51 XZ 9qnc C #2.3
---
Chain | Description
C | No description available
Chain information for AP1 RAD51 XZ 9qnc D #2.4
---
Chain | Description
D | No description available
Chain information for AP1 RAD51 XZ 9qnc E #2.5
---
Chain | Description
E | No description available
Chain information for AP1 RAD51 XZ 9qnc F #2.6
---
Chain | Description
F | No description available
Chain information for AP1 RAD51 XZ 9qnc G #2.7
---
Chain | Description
G | No description available
Chain information for AP1 RAD51 XZ 9qnc H #2.8
---
Chain | Description
H | No description available
Chain information for AP1 RAD51 XZ 9qnc I #2.9
---
Chain | Description
I | No description available
Chain information for AP1 RAD51 XZ 9qnc J #2.10
---
Chain | Description
J | No description available
Chain information for AP1 RAD51 XZ 9qnc K #2.11
---
Chain | Description
K | No description available
Chain information for AP1 RAD51 XZ 9qnc L #2.12
---
Chain | Description
L | No description available
Chain information for AP1 RAD51 XZ 9qnc Z #2.13
---
Chain | Description
Z | No description available
> save "/Users/anz/Desktop/P-motifs 260221.cxs"
> hide #!3 models
> cartoon #2
> rename #2.13 DNA
> hide #!2.1 models
> show #!2.1 models
> hide #!2.1 models
> show #!2.1 models
> hide #2.2 models
> show #2.2 models
> rename #2.1,3,5,7,9,11 RAD51
> rename #2.1 RAD51 1
Expected a keyword
> rename #2.1 "RAD51 1"
> rename #2.3 "RAD51 2"
> rename #2.5 "RAD51 3"
> rename #2.7 "RAD51 4"
> hide #!2.7 models
> show #!2.7 models
> hide #!2.7 models
> show #!2.7 models
> rename #2.9 "RAD51 5"
> rename #2.11 "RAD51 6"
> rename #2.2 "AP1 pep 1"
> rename #2.4 "AP1 pep 2"
> select down
1187 atoms, 1216 bonds, 150 residues, 1 model selected
> select down
1187 atoms, 1216 bonds, 150 residues, 1 model selected
> rename #2.6 "AP1 pep 3"
> rename #2.8 "AP1 pep 4"
> rename #2.10 "AP1 pep 5"
> rename #2.12 "AP1 pep 6"
> help mmaker
> mmaker #2.3 to #3.2 bring #2.1,2,4-13
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 DMC1, chain B (#3.2) with RAD51 2, chain C (#2.3), sequence
alignment score = 1035.4
RMSD between 283 pruned atom pairs is 0.842 angstroms; (across all 312 pairs:
1.769)
> ~cartoon #2.1,2,5-13
> cartoon #2.1,2,5-13
> show #!3 models
> ~cartoon #2.1,2,5-13
> color #2.4 red
> save "/Users/anz/Desktop/P-motifs 260221.cxs"
> hide #7
> ~cartoon #7
> ~select
Nothing selected
> ~cartoon @2.3
> cartoon hide @2.3
Expected an atoms specifier or a keyword
> ~cartoon #2.3
> select ~sel & ##selected
Nothing selected
> color #2.4 magenta
Cell requested for row 2 is out of bounds for table with 46 rows! Resizing
table model.
> rename #2 "AP1 RAD51 Cryo 9qnc"
> cartoon #3.8
> select clear
> show #2.4:335-338
> show #2.4:335-338 stick
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show #2.4:335-338 atoms
> help show
> style ball
Changed 90630 atom styles
> show #2.4:335-338 atoms
> show #2.4:334-338 atoms
> label #2.4:335-338
> help label
> label #5.1:95-104
> select ~sel & ##selected
Nothing selected
> label #5.1:95-104 color red
> save "/Users/anz/Desktop/P-motifs 260221.cxs"
> open /Users/anz/Downloads/fold_mnd1_rad51/fold_mnd1_rad51_model_0.cif
Chain information for fold_mnd1_rad51_model_0.cif #8
---
Chain | Description
A | .
B | .
Computing secondary structure
> close #8
> help label
> label listfonts
336 fonts available:
.Apple Color Emoji UI
.Apple Symbols Fallback
.AppleHongKongChineseFont
.AppleIndicFont
.AppleJapaneseFont
.AppleKoreanFont
.AppleMacaoChineseFont
.AppleSimplifiedChineseFont
.AppleSystemFallback
.AppleSystemUIFont
.AppleTraditionalChineseFont
.AppleUrduFont
.Lucida Grande UI
.SF Arabic
.SF Armenian
.SF Georgian
.SF Hebrew
.ThonburiUI
.Times Fallback
Academy Engraved LET
Adelle Sans Devanagari
AkayaKanadaka
AkayaTelivigala
Al Bayan
Al Nile
Al Tarikh
Aller
Aller Display
American Typewriter
Andale Mono
Annai MN
Apple Braille
Apple Chancery
Apple Color Emoji
Apple LiGothic
Apple LiSung
Apple SD Gothic Neo
Apple Symbols
AppleGothic
AppleMyungjo
Arial
Arial Black
Arial Hebrew
Arial Hebrew Scholar
Arial Narrow
Arial Rounded MT Bold
Arial Unicode MS
Arima Koshi
Arima Madurai
Avenir
Avenir Next
Avenir Next Condensed
Ayuthaya
BM Dohyeon
BM Hanna 11yrs Old
BM Hanna Air
BM Hanna Pro
BM Jua
BM Kirang Haerang
BM Yeonsung
Baghdad
Bai Jamjuree
Baloo 2
Baloo Bhai 2
Baloo Bhaijaan
Baloo Bhaina 2
Baloo Chettan 2
Baloo Da 2
Baloo Paaji 2
Baloo Tamma 2
Baloo Tammudu 2
Baloo Thambi 2
Bangla MN
Bangla Sangam MN
Baoli SC
Baoli TC
Baskerville
Beirut
BiauKaiHK
BiauKaiTC
Big Caslon
Bodoni 72
Bodoni 72 Oldstyle
Bodoni 72 Smallcaps
Bodoni Ornaments
Bradley Hand
Brush Script MT
Cambay Devanagari
Chakra Petch
Chalkboard
Chalkboard SE
Chalkduster
Charm
Charmonman
Charter
Cochin
Comic Sans MS
Copperplate
Corsiva Hebrew
Courier New
DIN Alternate
DIN Condensed
Damascus
DecoType Naskh
Devanagari MT
Devanagari Sangam MN
Didot
Diwan Kufi
Diwan Thuluth
Euphemia UCAS
Fahkwang
Farah
Farisi
Futura
GB18030 Bitmap
Galvji
Geeza Pro
Geneva
Georgia
Gill Sans
Gotu
Grantha Sangam MN
Gujarati MT
Gujarati Sangam MN
GungSeo
Gurmukhi MN
Gurmukhi MT
Gurmukhi Sangam MN
Hannotate SC
Hannotate TC
HanziPen SC
HanziPen TC
HeadLineA
Hei
Heiti SC
Heiti TC
Helvetica
Helvetica Neue
Herculanum
Hiragino Maru Gothic ProN
Hiragino Mincho ProN
Hiragino Sans
Hiragino Sans GB
Hiragino Sans TC
Hoefler Text
Hubballi
ITF Devanagari
ITF Devanagari Marathi
Impact
InaiMathi
Jaini
Jaini Purva
K2D
Kai
Kailasa
Kaiti SC
Kaiti TC
Kannada MN
Kannada Sangam MN
Katari
Kavivanar
Kefa III
Khmer MN
Khmer Sangam MN
Klee
KoHo
Kodchasan
Kohinoor Bangla
Kohinoor Devanagari
Kohinoor Gujarati
Kohinoor Telugu
Kokonor
Krub
Krungthep
KufiStandardGK
Lahore Gurmukhi
Lantinghei SC
Lantinghei TC
Lao MN
Lao Sangam MN
Lava Devanagari
Lava Kannada
Lava Telugu
LiHei Pro
LiSong Pro
Libian SC
Libian TC
LingWai SC
LingWai TC
Lucida Grande
Luminari
Maku
Malayalam MN
Malayalam Sangam MN
Mali
Marker Felt
Menlo
Microsoft Sans Serif
Mishafi
Mishafi Gold
Modak
Monaco
Montserrat
Mshtakan
Mukta
Mukta Mahee
Mukta Malar
Mukta Vaani
Muna
Myanmar MN
Myanmar Sangam MN
Nadeem
Nanum Brush Script
Nanum Gothic
Nanum Myeongjo
Nanum Pen Script
New Peninim MT
Niramit
Noteworthy
Noto Nastaliq Urdu
Noto Sans Armenian
Noto Sans Batak
Noto Sans Kannada
Noto Sans Myanmar
Noto Sans NKo
Noto Sans Oriya
Noto Sans Syriac
Noto Sans Tagalog
Noto Sans Zawgyi
Noto Serif Kannada
Noto Serif Myanmar
October Compressed Devanagari
October Compressed Tamil
October Condensed Devanagari
October Condensed Tamil
October Devanagari
October Tamil
Optima
Oriya MN
Oriya Sangam MN
Osaka
PCMyungjo
PSL Ornanong Pro
PT Mono
PT Sans
PT Sans Caption
PT Sans Narrow
PT Serif
PT Serif Caption
Padyakke Expanded One
Palatino
Papyrus
Party LET
Phosphate
PilGi
PingFang HK
PingFang MO
PingFang SC
PingFang TC
Plantagenet Cherokee
Raanana
Rockwell
STFangsong
STHeiti
STIX Two Math
STIX Two Text
STKaiti
STSong
Sama Devanagari
Sama Gujarati
Sama Gurmukhi
Sama Kannada
Sama Malayalam
Sama Tamil
Sana
Sarabun
Sathu
Savoye LET
Shobhika
Shree Devanagari 714
SignPainter
Silom
SimSong
Sinhala MN
Sinhala Sangam MN
Skia
Snell Roundhand
Songti SC
Songti TC
Srisakdi
Sukhumvit Set
Symbol
Tahoma
Tamil MN
Tamil Sangam MN
Telugu MN
Telugu Sangam MN
Thonburi
Times New Roman
Tiro Bangla
Tiro Devanagari Hindi
Tiro Devanagari Marathi
Tiro Devanagari Sanskrit
Tiro Gurmukhi
Tiro Kannada
Tiro Tamil
Tiro Telugu
Toppan Bunkyu Gothic
Toppan Bunkyu Midashi Gothic
Toppan Bunkyu Midashi Mincho
Toppan Bunkyu Mincho
Trattatello
Trebuchet MS
Tsukushi A Round Gothic
Tsukushi B Round Gothic
Verdana
Waseem
Wawati SC
Wawati TC
Webdings
Wingdings
Wingdings 2
Wingdings 3
Xingkai SC
Xingkai TC
YuGothic
YuKyokasho
YuKyokasho Yoko
YuMincho
YuMincho +36p Kana
Yuanti SC
Yuanti TC
Yuppy SC
Yuppy TC
Zapf Dingbats
Zapfino
> label #5.1:95-104 color red height 1.5 font "Arial Black"
> label #5.1:95-104 color red height 1 font "Arial Black"
> label #2.4:333-340 hight 1 font 'Arial Black'
Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword
> label #2.4:335-338
> label #2.4:335-338 font "Arial Black"
> label #2.4:331-340 font "Arial Black"
> label #2.4:331-340 font "Arial Black" color magenta
> show #2.4:333
> show #5.1:102
> show #3.2:102
> ~show #3.2:102
> ~show #3.2:117-119
> show #3.2:117-119
Unsupported scale factor (0.000000) detected on Display1
[Repeated 2 time(s)]
> save "/Users/anz/Desktop/P-motifs 260223 GLS.cxs"
——— End of log from Tue Feb 24 10:12:16 2026 ———
> view name session-start
opened ChimeraX session
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M4
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PySide6 6.10.1, Qt 6.10.1
Qt runtime version: 6.10.1
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac16,12
Model Number: Z1GS000EYN/A
Chip: Apple M4
Total Number of Cores: 10 (4 Performance and 6 Efficiency)
Memory: 24 GB
System Firmware Version: 13822.81.10
OS Loader Version: 13822.81.10
Software:
System Software Overview:
System Version: macOS 26.3.1 (a) (25D771280a)
Kernel Version: Darwin 25.3.0
Time since boot: 3 days, 15 hours, 25 minutes
Graphics/Displays:
Apple M4:
Chipset Model: Apple M4
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
HP Z23n:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
accessible-pygments: 0.0.5
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.1
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.18.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 4.0.0
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.2
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.64.1
ChimeraX-AtomicLibrary: 14.2.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4.1
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.1
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.12.dev202602270247
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.2
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.8.2
ChimeraX-Label: 1.3
ChimeraX-LightingGUI: 1.0
ChimeraX-ListInfo: 1.3.1
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.2.0
ChimeraX-MDcrds: 2.18
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.5
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.23
ChimeraX-ModelPanel: 1.6.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.4
ChimeraX-OpenFold: 1.0
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.12
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.5.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.8
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.12
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.5
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SNFG: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.50.3
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.6.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.4
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.2.4
debugpy: 1.8.20
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 7.1.0
ipython: 9.9.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.8.0
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.1
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
OpenMM: 8.4.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.6
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.9.2
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
pydantic-settings: 2.13.1
pydantic_core: 2.41.5
pydata-sphinx-theme: 0.16.1
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.5.0
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PySide6: 6.10.1
PySide6_Addons: 6.10.1
PySide6_Essentials: 6.10.1
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.22
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2.1
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
shiboken6: 6.10.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8.3
Sphinx: 9.0.4
sphinx-autodoc-typehints: 3.6.1
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
sse-starlette: 3.2.0
stack-data: 0.6.3
starlette: 0.52.1
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.4
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
urllib3: 2.6.3
uvicorn: 0.41.0
wcwidth: 0.6.0
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
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