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Opened 10 months ago
Closed 10 months ago
#16546 closed defect (nonchimerax)
Silhouette outlines incorrect in saved image
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.4-x86_64-i386-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
when save the png file by using commands save XX.png transparentBackground true width XX, the saved image is not what I can see on the chimeraX window but messed up with bunches of outlines of the models at unexpected areas. It used to work well on my mac, but is now problematic. Not only in this version, is the same thing also happens in the other versions (1.8, or even older version) Please find attached image as a reference. I wish how to fix this problems, or is it a kind of bug.
Thank you so much!
Log:
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/airen/Dropbox/0_Tubulin_specific_chaperone/0_Structure_pool/ChimeraX/overall1.cxs
Opened Map2_TBC_DEG_beta_with_Edensity_cryosparc_P7J211_P22_J1017.mrc as #8,
grid size 350,350,350, pixel 0.59, shown at level 0.272, step 1, values
float32
Opened Map1_cryosparc_P7_J200_map_sharp_deepEMhancer.mrc as #9, grid size
350,350,350, pixel 0.59, shown at level 0.249, step 2, values float32
Opened Map3_cryosparc_P22_J1999_map_sharp_deepEM.mrc as #10, grid size
300,300,300, pixel 0.76, shown at level 0.161, step 2, values float32
Opened Map4_cryosparc_P22_J2169_map_sharp_patched_deepEM.mrc as #11, grid size
320,320,320, pixel 1.02, shown at level 0.17, step 2, values float32
Opened Map5_cryosparc_P22_J2345_map_sharp (1).mrc as #12, grid size
256,256,256, pixel 1.08, shown at level 0.213, step 1, values float32
Opened Map6_cryosparc_P22_J2347_map_sharp (2).mrc as #13, grid size
256,256,256, pixel 1.08, shown at level 0.314, step 1, values float32
Log from Thu Nov 14 19:18:36 2024UCSF ChimeraX version: 1.9.dev202410220943
(2024-10-22)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/shroh/Dropbox/TBC/0_Model_pool/ChimeraX/interface1.cxs
Log from Thu Nov 14 13:28:54 2024UCSF ChimeraX version: 1.9.dev202410220943
(2024-10-22)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/shroh/Dropbox/TBC/interface_alpha_beta_pisa.cxs
Log from Thu Oct 24 14:16:16 2024UCSF ChimeraX version: 1.9.dev202410220943
(2024-10-22)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/shroh/Dropbox/TBC/interface_4.cxs
Log from Tue Oct 22 23:09:51 2024UCSF ChimeraX version: 1.9.dev202410220943
(2024-10-22)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/shroh/Dropbox/TBC/interface_3.cxs format session
Log from Tue Oct 22 22:13:54 2024 Startup Errors
---
errors | Bundle 'ChimeraX-Clipper' custom initialization failed
Bundle 'ChimeraX-ISOLDE' custom initialization failed
warnings | Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 501, in get_module
m = importlib.import_module(self.package_name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/importlib/__init__.py",
line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "<frozen importlib._bootstrap>", line 1204, in _gcd_import
File "<frozen importlib._bootstrap>", line 1176, in _find_and_load
File "<frozen importlib._bootstrap>", line 1147, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 690, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 940, in exec_module
File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
File "/Users/shroh/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/clipper/__init__.py", line 32, in <module>
__version__ = _version()
^^^^^^^^^^
File "/Users/shroh/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/clipper/__init__.py", line 30, in _version
return pkg_resources.require('ChimeraX-Clipper')[0].version
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/pkg_resources/__init__.py", line 937, in require
needed = self.resolve(parse_requirements(requirements))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/pkg_resources/__init__.py", line 798, in resolve
dist = self._resolve_dist(
^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/pkg_resources/__init__.py", line 844, in _resolve_dist
raise VersionConflict(dist, req).with_context(dependent_req)
pkg_resources.ContextualVersionConflict: (ChimeraX-AtomicLibrary 14.0.5
(/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages), Requirement.parse('ChimeraX-AtomicLibrary~=12.0'), {'ChimeraX-
Clipper'})
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 375, in initialize
api = self._get_api(session.logger)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 520, in _get_api
m = self.get_module()
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 503, in get_module
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-
Clipper's module: (ChimeraX-AtomicLibrary 14.0.5
(/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages), Requirement.parse('ChimeraX-AtomicLibrary~=12.0'), {'ChimeraX-
Clipper'})
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 501, in get_module
m = importlib.import_module(self.package_name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/importlib/__init__.py",
line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "<frozen importlib._bootstrap>", line 1204, in _gcd_import
File "<frozen importlib._bootstrap>", line 1176, in _find_and_load
File "<frozen importlib._bootstrap>", line 1147, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 690, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 940, in exec_module
File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
File "/Users/shroh/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/__init__.py", line 51, in <module>
__version__ = _version()
^^^^^^^^^^
File "/Users/shroh/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/__init__.py", line 49, in _version
return pkg_resources.require('ChimeraX-ISOLDE')[0].version
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/pkg_resources/__init__.py", line 937, in require
needed = self.resolve(parse_requirements(requirements))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/pkg_resources/__init__.py", line 798, in resolve
dist = self._resolve_dist(
^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/pkg_resources/__init__.py", line 844, in _resolve_dist
raise VersionConflict(dist, req).with_context(dependent_req)
pkg_resources.ContextualVersionConflict: (ChimeraX-AtomicLibrary 14.0.5
(/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages), Requirement.parse('ChimeraX-AtomicLibrary~=12.0'), {'ChimeraX-
ISOLDE', 'ChimeraX-Clipper'})
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 375, in initialize
api = self._get_api(session.logger)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 520, in _get_api
m = self.get_module()
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 503, in get_module
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-ISOLDE's
module: (ChimeraX-AtomicLibrary 14.0.5
(/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages), Requirement.parse('ChimeraX-AtomicLibrary~=12.0'), {'ChimeraX-
ISOLDE', 'ChimeraX-Clipper'})
UCSF ChimeraX version: 1.8rc202405282004 (2024-05-28)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/shroh/Dropbox/TBC/0_DEG_C_abTub/full_tbc.pdb
Chain information for full_tbc.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
> hide atoms
> show cartoons
> set bgColor white
> color chain #1/A red
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color red #1/A
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color red chain #1/A
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color red A
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color red #1
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #1/A red
> color #1/A 01befe
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #1/A 01BEFE
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> select /A:1177
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
124 atoms, 123 bonds, 15 residues, 1 model selected
> select up
9312 atoms, 9493 bonds, 1192 residues, 1 model selected
> ui tool show "Color Actions"
> color sel deep sky blue
> color #1/A deep sky blue
> ui tool show "Color Actions"
> color #1/A deep sky blue
> color #1/B gold
> color #1/C orange
> ui tool show "Color Actions"
> color #1/A deep sky blue
> color #1/B gold
> color #1/C orange
> color #1/D deep pink
> color #1/E lime
> ui tool show "Color Actions"
[Repeated 2 time(s)]
> color sel medium slate blue
> color #1/A deep sky blue
> color #1/B gold
> color #1/C orange
> color #1/D deep pink
> color #1/E lime
> color #1/F medium slate blue
> lighting full
[Repeated 1 time(s)]
> lighting soft
> lighting simple
> lighting soft
> lighting full
> select clear
> color #1/A deep sky blue
> color #1/B gold
> color #1/C orange red
> color #1/D deep pink
> color #1/E lime
> color #1/F medium slate blue
> color #1/A deep sky blue
> color #1/B dark goldenrod
> color #1/C orange red
> color #1/D deep pink
> color #1/E lime
> color #1/F medium slate blue
> color #1/A deep sky blue
> color #1/B deeppink gold; color #1/C orange red; color #1/D deep pink; color
> #1/E lime; color #1/F medium slate blue
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #1/A deep sky blue
> color #1/B light goldenrod yellow
> color #1/C orange red
> color #1/D deep pink
> color #1/E lime
> color #1/F medium slate blue
> select clear
[Repeated 1 time(s)]Drag select of 12 residues
> select up
178 atoms, 176 bonds, 24 residues, 1 model selected
> select up
1467 atoms, 1490 bonds, 184 residues, 1 model selected
> ui tool show "Color Actions"
> color sel magenta
> color sel hot pink
> color sel purple
> color sel cornflower blue
> color sel medium blue
> color sel medium slate blue
> color sel slate blue
Drag select of 11 residues
> select up
371 atoms, 373 bonds, 48 residues, 1 model selected
> select up
3524 atoms, 3603 bonds, 451 residues, 1 model selected
> color sel cornflower blue
> select /F:48
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
21 atoms, 20 bonds, 3 residues, 1 model selected
> select up
3486 atoms, 3562 bonds, 444 residues, 1 model selected
> color sel orange red
Drag select of 10 residues
> select up
195 atoms, 199 bonds, 27 residues, 1 model selected
> select up
4176 atoms, 4256 bonds, 527 residues, 1 model selected
> color sel magenta
> select clear
Drag select of 18 residues
> select up
696 atoms, 707 bonds, 85 residues, 1 model selected
> select up
9312 atoms, 9493 bonds, 1192 residues, 1 model selected
> color sel blue
> select clear
> color #1/A FF0000
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #1/A #FF0000
> color #1/A #0015FF
> color #1/B #FF00A1
> color #1/C #90FE00
> color #1/D #8400FF
> color #1/E 00FFF7; color #1/F FF7300
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #1/A #0015FF
> color #1/B #FF00A1
> color #1/C #90FE00
> color #1/D #8400FF
> color #1/E #00FFF7
> color #1/F #FF7300
> color #FF5733 #1/A # Color chain A with vibrant red
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #FFC300 #1/B # Color chain B with bright yellow
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #00FFFF #1/C # Color chain C with cyan blue
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #DA70D6 #1/D # Color chain D with electric purple
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #32CD32 #1/E # Color chain E with lime green
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #FF69B4 #1/F # Color chain F with hot pink
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #FF4500 #1/G # Color chain G with bright orange
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #87CEEB #1/H # Color chain H with sky blue
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #FF00FF #1/I # Color chain I with bright magenta
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #39FF14 #1/J # Color chain J with neon green
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #1/A #FF5733
> color #1/B #FFC300
> color #1/C #00FFFF
> color #1/D #DA70D6
> color #1/E #32CD32
> color #1/F #FF69B4
> color #1/G #FF4500
> color #1/H #87CEEB
> color #1/I #FF00FF
> color #1/J #39FF14
> color #1/A #4169E1
> color #1/B #87CEEB
> color #1/C #00FFFF
> color #1/D #1E90FF
> color #1/E #00BFFF
> color #1/F #7DF9FF
> color #1/G #40E0D0
> color #1/H #4682B4
> color #1/I #20B2AA
> color #1/J #008080
> olor #1/A #4169E1; color #1/B #00BFFF; color #1/C #1E90FF; color #1/D
> #4682B4; color #1/E #7DF9FF; color #1/F #6495ED; color #1/G #7B68EE; color
> #1/H #B0C4DE; color #1/I #6A5ACD; color #1/J #008080
Unknown command: olor #1/A #4169E1; color #1/B #00BFFF; color #1/C #1E90FF;
color #1/D #4682B4; color #1/E #7DF9FF; color #1/F #6495ED; color #1/G
#7B68EE; color #1/H #B0C4DE; color #1/I #6A5ACD; color #1/J #008080
> color #1/A #4169E1
> color #1/B #00BFFF
> color #1/C #1E90FF
> color #1/D #4682B4
> color #1/E #7DF9FF
> color #1/F #6495ED
> color #1/G #7B68EE
> color #1/H #B0C4DE
> color #1/I #6A5ACD
> color #1/J #008080
> color #1/A #4169E1
> color #1/B #00BFFF
> color #1/C #1E90FF
> color #1/D #4682B4
> color #1/E #7DF9FF
> color #1/F #FF69B4
> color #1/G #FF4500
> color #1/H #87CEEB
> color #1/I #FF00FF
> color #1/J #39FF14
> color #1/A #4169E1
> color #1/B #00BFFF
> color #1/C #1E90FF
> color #1/D #4682B4
> color #1/E #40E0D0
> color #1/F #BF00FF
> color #1/G #FF69B4
> color #1/H #FF4500
> color #1/I #87CEEB
> color #1/J #FF00FF
> color #1/K #39FF14
> rainbow chains
Drag select of 12 residues
> select up
240 atoms, 247 bonds, 32 residues, 1 model selected
> select up
4176 atoms, 4256 bonds, 527 residues, 1 model selected
> color sel orange red
> ui tool show "Color Actions"
> color sel magenta
> color sel royal blue
> color sel deep sky blue
> color sel cyan
> color sel dark turquoise
> color sel medium spring green
> color sel dodger blue
> color sel turquoise
> color sel medium turquoise
> color sel light sea green
> color sel dark cyan
[Repeated 1 time(s)]
> color sel medium aquamarine
> color sel teal
> color sel steel blue
> color sel cadet blue
> color sel light slate gray
> color sel dark orchid
> color sel dark magenta
> color sel purple
> color sel medium purple
> color sel midnight blue
> color sel dark slate gray
> color sel medium slate blue
> color sel slate blue
> color sel dark slate blue
> color sel rebecca purple
> color sel deep pink
> color sel dark violet
> color sel dodger blue
> color sel peru
> color sel light salmon
> color sel red
> color sel orange red
> color sel crimson
> color sel dark red
> color sel maroon
> color sel fire brick
> color sel tomato
> color sel royal blue
> color sel magenta
> color sel deep pink
> color sel dark violet
> color sel hot pink
> color sel blue violet
> color sel orchid
> color sel medium orchid
> color sel medium violet red
> color sel dark orchid
> color sel dark magenta
Drag select of 24 residues
> select up
725 atoms, 742 bonds, 90 residues, 1 model selected
> select up
3524 atoms, 3603 bonds, 451 residues, 1 model selected
> color sel blue
Drag select of 30 residues
> select up
313 atoms, 314 bonds, 43 residues, 1 model selected
> select up
9312 atoms, 9493 bonds, 1192 residues, 1 model selected
> color sel cyan
> select clear
Drag select of 20 residues
> select up
240 atoms, 247 bonds, 32 residues, 1 model selected
> select up
4176 atoms, 4256 bonds, 527 residues, 1 model selected
> color sel orange red
> color sel hot pink
> select clear
Drag select of 32 residues
> select up
530 atoms, 541 bonds, 71 residues, 1 model selected
> select up
4176 atoms, 4256 bonds, 527 residues, 1 model selected
> color sel magenta
> select clear
Drag select of 23 residues
> select up
281 atoms, 280 bonds, 35 residues, 1 model selected
> select up
2757 atoms, 2803 bonds, 346 residues, 1 model selected
> color sel lime
> color sel forest green
> color sel lime
> select /B:100
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
130 atoms, 129 bonds, 15 residues, 1 model selected
> select up
1467 atoms, 1490 bonds, 184 residues, 1 model selected
> ui tool show "Color Actions"
> color sel royal blue
> color sel yellow
> color sel gold
> color sel goldenrod
> select clear
Drag select of 19 residues
> select up
310 atoms, 314 bonds, 41 residues, 1 model selected
> select up
4176 atoms, 4256 bonds, 527 residues, 1 model selected
> color sel lime
Drag select of 14 residues
> select up
404 atoms, 404 bonds, 49 residues, 1 model selected
> select up
2757 atoms, 2803 bonds, 346 residues, 1 model selected
> color sel magenta
> select clear
> lighting full
[Repeated 1 time(s)]
> lighting soft
> lighting simple
> lighting full
> graphics silhouettes true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting flat
[Repeated 1 time(s)]
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting flat
> lighting full
> lighting shadows false
> ui tool show "Side View"
> color list
No custom colors.
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
, dark olive green
, dark orange
, dark orchid
, dark red
, dark salmon
, dark sea green
, dark seagreen
, dark slate blue
, dark slate gray
, dark slate grey
, dark turquoise
, dark violet
, darkblue
, darkcyan
, darkgoldenrod
, darkgray
, darkgreen
, darkgrey
, darkkhaki
, darkmagenta
, darkolivegreen
, darkorange
, darkorchid
, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
, deep skyblue
, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
, forestgreen
, fuchsia
, gainsboro
, ghost white
, ghostwhite
, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
, indianred
, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
, light blue
, light coral
, light cyan
, light goldenrod yellow
, light gray
, light green
, light grey
, light pink
, light salmon
, light sea green
, light seagreen
, light sky blue
, light skyblue
, light slate gray
, light slate grey
, light steel blue
, light yellow
, lightblue
, lightcoral
, lightcyan
, lightgoldenrodyellow
, lightgray
, lightgreen
, lightgrey
, lightpink
, lightsalmon
, lightseagreen
, lightskyblue
, lightslategray
, lightslategrey
, lightsteelblue
, lightyellow
, lime
, lime green
, limegreen
, linen
, magenta
, maroon
, medium aquamarine
, medium blue
, medium orchid
, medium purple
, medium sea green
, medium seagreen
, medium slate blue
, medium spring green
, medium turquoise
, medium violet red
, mediumaquamarine
, mediumblue
, mediumorchid
, mediumpurple
, mediumseagreen
, mediumslateblue
, mediumspringgreen
, mediumturquoise
, mediumvioletred
, midnight blue
, midnightblue
, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
, orange
, orange red
, orangered
, orchid
, pale goldenrod
, pale green
, pale turquoise
, pale violet red
, palegoldenrod
, palegreen
, paleturquoise
, palevioletred
, papaya whip
, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
, powder blue
, powderblue
, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
, royalblue
, saddle brown
, saddlebrown
, salmon
, sandy brown
, sandybrown
, sea green
, seagreen
, seashell
, sienna
, silver
, sky blue
, skyblue
, slate blue
, slate gray
, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
.
> color list #1
Expected one of 'all', 'builtin', or 'custom' or a keyword
> color #1
> color list
No custom colors.
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
, dark olive green
, dark orange
, dark orchid
, dark red
, dark salmon
, dark sea green
, dark seagreen
, dark slate blue
, dark slate gray
, dark slate grey
, dark turquoise
, dark violet
, darkblue
, darkcyan
, darkgoldenrod
, darkgray
, darkgreen
, darkgrey
, darkkhaki
, darkmagenta
, darkolivegreen
, darkorange
, darkorchid
, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
, deep skyblue
, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
, forestgreen
, fuchsia
, gainsboro
, ghost white
, ghostwhite
, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
, indianred
, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
, light blue
, light coral
, light cyan
, light goldenrod yellow
, light gray
, light green
, light grey
, light pink
, light salmon
, light sea green
, light seagreen
, light sky blue
, light skyblue
, light slate gray
, light slate grey
, light steel blue
, light yellow
, lightblue
, lightcoral
, lightcyan
, lightgoldenrodyellow
, lightgray
, lightgreen
, lightgrey
, lightpink
, lightsalmon
, lightseagreen
, lightskyblue
, lightslategray
, lightslategrey
, lightsteelblue
, lightyellow
, lime
, lime green
, limegreen
, linen
, magenta
, maroon
, medium aquamarine
, medium blue
, medium orchid
, medium purple
, medium sea green
, medium seagreen
, medium slate blue
, medium spring green
, medium turquoise
, medium violet red
, mediumaquamarine
, mediumblue
, mediumorchid
, mediumpurple
, mediumseagreen
, mediumslateblue
, mediumspringgreen
, mediumturquoise
, mediumvioletred
, midnight blue
, midnightblue
, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
, orange
, orange red
, orangered
, orchid
, pale goldenrod
, pale green
, pale turquoise
, pale violet red
, palegoldenrod
, palegreen
, paleturquoise
, palevioletred
, papaya whip
, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
, powder blue
, powderblue
, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
, royalblue
, saddle brown
, saddlebrown
, salmon
, sandy brown
, sandybrown
, sea green
, seagreen
, seashell
, sienna
, silver
, sky blue
, skyblue
, slate blue
, slate gray
, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
.
> color list chains
Expected one of 'all', 'builtin', or 'custom' or a keyword
> color list chain
Expected one of 'all', 'builtin', or 'custom' or a keyword
> color list atoms
Expected one of 'all', 'builtin', or 'custom' or a keyword
> color list atom
Expected one of 'all', 'builtin', or 'custom' or a keyword
> color list #1
Expected one of 'all', 'builtin', or 'custom' or a keyword
> color list #1/A
Expected one of 'all', 'builtin', or 'custom' or a keyword
> bash color list
Unknown command: bash color list
> bash; color list
Unknown command: bash; color list
> color list atoms #1
Expected one of 'all', 'builtin', or 'custom' or a keyword
> color list builtin
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
, dark olive green
, dark orange
, dark orchid
, dark red
, dark salmon
, dark sea green
, dark seagreen
, dark slate blue
, dark slate gray
, dark slate grey
, dark turquoise
, dark violet
, darkblue
, darkcyan
, darkgoldenrod
, darkgray
, darkgreen
, darkgrey
, darkkhaki
, darkmagenta
, darkolivegreen
, darkorange
, darkorchid
, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
, deep skyblue
, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
, forestgreen
, fuchsia
, gainsboro
, ghost white
, ghostwhite
, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
, indianred
, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
, light blue
, light coral
, light cyan
, light goldenrod yellow
, light gray
, light green
, light grey
, light pink
, light salmon
, light sea green
, light seagreen
, light sky blue
, light skyblue
, light slate gray
, light slate grey
, light steel blue
, light yellow
, lightblue
, lightcoral
, lightcyan
, lightgoldenrodyellow
, lightgray
, lightgreen
, lightgrey
, lightpink
, lightsalmon
, lightseagreen
, lightskyblue
, lightslategray
, lightslategrey
, lightsteelblue
, lightyellow
, lime
, lime green
, limegreen
, linen
, magenta
, maroon
, medium aquamarine
, medium blue
, medium orchid
, medium purple
, medium sea green
, medium seagreen
, medium slate blue
, medium spring green
, medium turquoise
, medium violet red
, mediumaquamarine
, mediumblue
, mediumorchid
, mediumpurple
, mediumseagreen
, mediumslateblue
, mediumspringgreen
, mediumturquoise
, mediumvioletred
, midnight blue
, midnightblue
, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
, orange
, orange red
, orangered
, orchid
, pale goldenrod
, pale green
, pale turquoise
, pale violet red
, palegoldenrod
, palegreen
, paleturquoise
, palevioletred
, papaya whip
, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
, powder blue
, powderblue
, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
, royalblue
, saddle brown
, saddlebrown
, salmon
, sandy brown
, sandybrown
, sea green
, seagreen
, seashell
, sienna
, silver
, sky blue
, skyblue
, slate blue
, slate gray
, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
.
> color name
Missing or invalid "name" argument: Expected a text string
> color name cname
Missing or invalid "color" argument: Missing color name or specifier
> color name #1/A
Missing or invalid "color" argument: Missing color name or specifier
> color name red
Missing or invalid "color" argument: Missing color name or specifier
> color show
Illegal color name: ""
> color show #1
Illegal color name: "#1"
> color name all
Missing or invalid "color" argument: Missing color name or specifier
> Color #1/E blue; color #1/F red; color #1/A cyan;color #1/C green; color
> #1/B goldtan; color #1/D purple
Unknown command: Color #1/E blue; color #1/F red; color #1/A cyan;color #1/C
green; color #1/B goldtan; color #1/D purple
> Color #1/E blue
Unknown command: Color #1/E blue
> Color blue #1/E
Unknown command: Color blue #1/E
> Color #1/E blue
Unknown command: Color #1/E blue
> color #1/E blue
> color #1/E blue
> color #1/F red
> color #1/A cyan
> color #1/C green
> color #1/B goldtan; color #1/D purple
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #1/E blue
> color #1/F red
> color #1/A cyan
> color #1/C light green
> color #1/B goldtan; color #1/D purple
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #1/E blue
> color #1/F red
> color #1/A cyan
> color #1/C lime
> color #1/B goldtan; color #1/D purple
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> cartoon style width 1.5 thickness 0.3
> cartoon style width 1.5 thickness 0.5
Drag select of 9 residues
> select up
412 atoms, 412 bonds, 50 residues, 1 model selected
> select up
2757 atoms, 2803 bonds, 346 residues, 1 model selected
> color sel hot pink
> select clear
Drag select of 51 residues
> select up
567 atoms, 572 bonds, 71 residues, 1 model selected
> select up
2757 atoms, 2803 bonds, 346 residues, 1 model selected
> color sel magenta
> select clear
> lighting depthCueStart 0.3 depthCueEnd 0.7
> lighting depthCue false
Drag select of 6 residues
> select up
145 atoms, 149 bonds, 20 residues, 1 model selected
> select up
3486 atoms, 3562 bonds, 444 residues, 1 model selected
> show sel surfaces
Drag select of 5 residues
> select up
116 atoms, 116 bonds, 15 residues, 1 model selected
> select up
3524 atoms, 3603 bonds, 451 residues, 1 model selected
> show sel surfaces
> select clear
Drag select of 17 residues
> select up
218 atoms, 224 bonds, 24 residues, 1 model selected
> select up
2757 atoms, 2803 bonds, 346 residues, 1 model selected
> cartoon style sel xsection oval modeHelix default
No visible Surface models selected
> save /Users/shroh/Dropbox/TBC/interface_3.cxs
——— End of log from Tue Oct 22 22:13:54 2024 ———
opened ChimeraX session
> select clear
> select /E:85@CB
1 atom, 1 residue, 1 model selected
> select add /F:36@CB
2 atoms, 2 residues, 2 models selected
> select up
21 atoms, 20 bonds, 2 residues, 3 models selected
> select up
167 atoms, 172 bonds, 21 residues, 3 models selected
> select up
7010 atoms, 7165 bonds, 895 residues, 3 models selected
> hide sel atoms
> hide sel cartoons
> hide sel surfaces
> show sel cartoons
> select clear
> ui tool show "Side View"
> save /Users/shroh/Desktop/tbc/surface1.tif pixelSize 0.1
> transparentBackground true
Directory "/Users/shroh/Desktop/tbc" does not exist
> save /Users/shroh/Desktop/tbc/surface1.tif pixelSize 0.1
> transparentBackground true
Drag select of 360 residues
Drag select of 21 residues
> select up
4714 atoms, 4792 bonds, 605 residues, 1 model selected
> select up
17712 atoms, 18042 bonds, 2249 residues, 1 model selected
> hide sel cartoons
> save /Users/shroh/Desktop/tbc/surface2.tif pixelSize 0.1
> transparentBackground true
> show sel cartoons
> select clear
Drag select of 1286 residues
> select up
12217 atoms, 12423 bonds, 1557 residues, 3 models selected
> select up
20546 atoms, 20951 bonds, 2617 residues, 3 models selected
> hide sel cartoons
> save /Users/shroh/Desktop/tbc/surface3.tif pixelSize 0.1
> transparentBackground true
> show sel cartoons
> select clear
Drag select of 24 residues
> select clear
Drag select of 741 residues
> select up
7261 atoms, 7395 bonds, 917 residues, 3 models selected
> select up
20498 atoms, 20914 bonds, 2614 residues, 3 models selected
> hide sel cartoons
Drag select of 28 residues
> select up
516 atoms, 520 bonds, 61 residues, 1 model selected
> select up
1467 atoms, 1490 bonds, 184 residues, 1 model selected
> hide sel cartoons
> save /Users/shroh/Desktop/tbc/surface4.tif pixelSize 0.1
> transparentBackground true
> select clear
> show cartoons
Drag select of 322 residues
Drag select of 37 residues
> select up
4080 atoms, 4148 bonds, 524 residues, 2 models selected
> select up
19769 atoms, 20155 bonds, 2516 residues, 2 models selected
> hide sel cartoons
Drag select of 267 residues
> select up
2556 atoms, 2607 bonds, 321 residues, 2 models selected
> select up
3486 atoms, 3562 bonds, 444 residues, 2 models selected
> hide sel cartoons
> save /Users/shroh/Desktop/tbc/surface5.tif pixelSize 0.1
> transparentBackground true
> select clear
> show cartoons
> select clear
[Repeated 2 time(s)]Drag select of 152 residues
> select up
1820 atoms, 1854 bonds, 231 residues, 1 model selected
> select up
4224 atoms, 4293 bonds, 530 residues, 1 model selected
> hide sel cartoons
Drag select of 184 residues
> hide sel cartoons
[Repeated 1 time(s)]
> select up
2026 atoms, 2060 bonds, 263 residues, 2 models selected
> select up
7700 atoms, 7859 bonds, 978 residues, 2 models selected
> hide sel cartoons
> select clear
Drag select of 3 residues
> select up
110 atoms, 111 bonds, 14 residues, 2 models selected
> select up
3486 atoms, 3562 bonds, 444 residues, 2 models selected
> hide sel cartoons
> save /Users/shroh/Desktop/tbc/surface5.tif pixelSize 0.1
> transparentBackground true
Drag select of 128 residues
> select up
1625 atoms, 1657 bonds, 208 residues, 1 model selected
> hide sel cartoons
Drag select of 76 residues
> hide sel cartoons
Drag select of 6 residues
> select up
69 atoms, 71 bonds, 9 residues, 1 model selected
> hide sel cartoons
Drag select of 1 residues
> select up
32 atoms, 31 bonds, 4 residues, 1 model selected
> hide sel cartoons
> save /Users/shroh/Desktop/tbc/surface6.tif pixelSize 0.1
> transparentBackground true
> select clear
> show cartoons
> view name front1
> select clear
Drag select of 3144 residues
> show sel surfaces
> select clear
Drag select of full_tbc.pdb_C SES surface, 10808 of 511950 triangles, 14
residues
Drag select of full_tbc.pdb_A SES surface, 65298 of 1014708 triangles,
full_tbc.pdb_B SES surface, 115407 of 179598 triangles, full_tbc.pdb_D SES
surface, 140865 of 396734 triangles, 350 residues
> select up
4269 atoms, 4355 bonds, 543 residues, 5 models selected
> select up
17712 atoms, 18042 bonds, 2249 residues, 5 models selected
> hide sel surfaces
> hide sel cartoons
> select clear
> hide cartoons
> save /Users/shroh/Desktop/tbc/surface7.tif pixelSize 0.1
> transparentBackground true
> show surfaces
> select clear
> select /E:58@CB
1 atom, 1 residue, 1 model selected
> select add /F:57@CA
2 atoms, 2 residues, 2 models selected
> select add /D:127@NH2
3 atoms, 3 residues, 3 models selected
> select add /A:278@NH1
4 atoms, 4 residues, 4 models selected
> select add /B:101@O
5 atoms, 5 residues, 5 models selected
> select add /D:270@CG
6 atoms, 6 residues, 6 models selected
> select up
50 atoms, 44 bonds, 6 residues, 6 models selected
> select up
556 atoms, 554 bonds, 71 residues, 6 models selected
> select up
20546 atoms, 20951 bonds, 2617 residues, 6 models selected
> hide sel surfaces
> save /Users/shroh/Desktop/tbc/surface8.tif pixelSize 0.1
> transparentBackground true
> show sel surfaces
> select subtract /E:361@OG1
20545 atoms, 20950 bonds, 2617 residues, 6 models selected
> select subtract /F:38@N
20544 atoms, 20948 bonds, 2617 residues, 6 models selected
> select subtract /A:238@NE
20543 atoms, 20946 bonds, 2617 residues, 6 models selected
> select subtract /B:105@CG
20542 atoms, 20944 bonds, 2617 residues, 6 models selected
> select up
20546 atoms, 20951 bonds, 2617 residues, 6 models selected
> select up
24754 atoms, 25241 bonds, 3145 residues, 6 models selected
> hide sel surfaces
> show sel surfaces
> select clear
Drag select of full_tbc.pdb_F SES surface, 62277 of 362194 triangles,
full_tbc.pdb_E SES surface, 28061 of 378186 triangles, full_tbc.pdb_A SES
surface, 120048 of 1014708 triangles, full_tbc.pdb_C SES surface, 174059 of
511950 triangles
> select up
4224 atoms, 530 residues, 7 models selected
> select up
24754 atoms, 25241 bonds, 3145 residues, 3 models selected
> hide sel surfaces
> show sel surfaces
> select clear
> select /C:275@CD2
1 atom, 1 residue, 1 model selected
> select add /E:37@N
2 atoms, 2 residues, 2 models selected
> select add /F:36@O
3 atoms, 3 residues, 3 models selected
> select up
29 atoms, 29 bonds, 3 residues, 4 models selected
> select up
291 atoms, 296 bonds, 40 residues, 4 models selected
> select up
11186 atoms, 11421 bonds, 1422 residues, 4 models selected
> hide sel surfaces
> select /B:105@CD
1 atom, 1 residue, 1 model selected
> select add /A:191@CG
2 atoms, 2 residues, 2 models selected
> select up
18 atoms, 16 bonds, 2 residues, 3 models selected
> select up
246 atoms, 245 bonds, 29 residues, 3 models selected
> select up
10779 atoms, 10983 bonds, 1376 residues, 3 models selected
> hide sel surfaces
> save /Users/shroh/Desktop/tbc/surface9.tif pixelSize 0.1
> transparentBackground true
> select clear
> show surfaces
> select /D:342@N
1 atom, 1 residue, 1 model selected
> select add /F:359@NE
2 atoms, 2 residues, 2 models selected
> select add /E:32@CB
3 atoms, 3 residues, 3 models selected
> select add /C:302@CB
4 atoms, 4 residues, 4 models selected
> select up
35 atoms, 32 bonds, 4 residues, 5 models selected
> select up
446 atoms, 453 bonds, 60 residues, 5 models selected
> select up
13943 atoms, 14224 bonds, 1768 residues, 5 models selected
> hide sel surfaces
> select /A:230@O
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
115 atoms, 117 bonds, 14 residues, 2 models selected
> select up
9312 atoms, 9493 bonds, 1192 residues, 2 models selected
> hide sel surfaces
> save /Users/shroh/Desktop/tbc/surface10.tif pixelSize 0.1
> transparentBackground true
> select clear
> show surfaces
> select /D:267@CD
1 atom, 1 residue, 1 model selected
> select add /F:45@CA
2 atoms, 2 residues, 2 models selected
> select add /E:36@O
3 atoms, 3 residues, 3 models selected
> select add /C:249@CA
4 atoms, 4 residues, 4 models selected
> select up
33 atoms, 29 bonds, 4 residues, 5 models selected
> select up
355 atoms, 355 bonds, 47 residues, 5 models selected
> select up
13943 atoms, 14224 bonds, 1768 residues, 5 models selected
> hide sel surfaces
> select /B:104@NH1
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 2 models selected
> select up
130 atoms, 129 bonds, 15 residues, 2 models selected
> select up
1467 atoms, 1490 bonds, 184 residues, 2 models selected
> hide sel surfaces
> save /Users/shroh/Desktop/tbc/surface11.tif pixelSize 0.1
> transparentBackground true
> save /Users/shroh/Dropbox/TBC/interface_4.cxs
——— End of log from Tue Oct 22 23:09:51 2024 ———
opened ChimeraX session
> select clear
> show cartoons
> color #1/E blue
> color #1/F red
> color #1/A cyan
> color #1/C lime
> color #1/B goldenrod
> color #1/D purple
Drag select of 11 residues
> color #1/E blue
> color #1/F red
> color #1/A cyan
> color #1/C lime
> color #1/B goldenrod
> color #1/D margenta
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #1/E blue
> color #1/F red
> color #1/A cyan
> color #1/C lime
> color #1/B goldenrod
> color #1/D magenta
> color #1/E blue
> color #1/F red
> color #1/A cyan
> color #1/C magenta
> color #1/B goldenrod
> color #1/D lime
Drag select of full_tbc.pdb_A SES surface, 3144 residues
> graphics silhouettes false
> graphics silhouettes true
> lighting full
> show sel surfaces
> lighting full
[Repeated 1 time(s)]
> lighting soft
[Repeated 1 time(s)]
> lighting simple
> lighting full
> lighting soft
[Repeated 1 time(s)]
> lighting full
[Repeated 2 time(s)]
> graphics silhouettes true width 4
> select clear
> toolshed show
> lighting
Intensity: 0.7
Direction: 0.577,-0.577,-0.577
Color: 100,100,100
Fill intensity: 0.3
Fill direction: -0.2,-0.2,-0.959
Fill color: 100,100,100
Ambient intensity: 0.8
Ambient color: 100,100,100
Depth cue: 1, start 0.5, end 1, color 100,100,100
Shadow: True (depth map size 2048, depth bias 0.005)
Multishadows: 64 (max 1024, depth map size 1024, depth bias 0.01)
> lighting gentle
> lighting full
> select clear
> select /F:37@O
1 atom, 1 residue, 1 model selected
> select up
10 atoms, 10 bonds, 1 residue, 2 models selected
> select up
95 atoms, 98 bonds, 13 residues, 2 models selected
> select up
3486 atoms, 3562 bonds, 444 residues, 2 models selected
> color (#!1 & sel) orange red
> select clear
> select /E:85@O
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
72 atoms, 74 bonds, 8 residues, 2 models selected
> select up
3524 atoms, 3603 bonds, 451 residues, 2 models selected
> ui tool show "Color Actions"
> color sel royal blue
> select clear
> select /A:137@CG2
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
96 atoms, 96 bonds, 13 residues, 2 models selected
> select up
9312 atoms, 9493 bonds, 1192 residues, 2 models selected
> color sel deep sky blue
> select clear
> select /A:177@O
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
110 atoms, 110 bonds, 15 residues, 2 models selected
> select up
9312 atoms, 9493 bonds, 1192 residues, 2 models selected
> color sel royal blue
> color sel cyan
> color sel dark turquoise
> color sel deep sky blue
> color sel cyan
> select clear
Drag select of full_tbc.pdb_C SES surface, 18577 of 511950 triangles, 18
residues
> select up
221 atoms, 228 bonds, 30 residues, 2 models selected
> select up
4176 atoms, 4256 bonds, 527 residues, 2 models selected
> color sel royal blue
> select /E:33@O
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
130 atoms, 131 bonds, 19 residues, 2 models selected
> select up
3524 atoms, 3603 bonds, 451 residues, 2 models selected
> color sel orange
> select clear
> select /E:85@CD
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
72 atoms, 74 bonds, 8 residues, 2 models selected
> select up
3524 atoms, 3603 bonds, 451 residues, 2 models selected
> color sel orange red
> select /F:56@O
1 atom, 1 residue, 1 model selected
> select up
4 atoms, 3 bonds, 1 residue, 2 models selected
> select up
15 atoms, 14 bonds, 3 residues, 2 models selected
> select up
3486 atoms, 3562 bonds, 444 residues, 2 models selected
> color sel orange
> select clear
> select /B:104@CG
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 2 models selected
> select up
130 atoms, 129 bonds, 15 residues, 2 models selected
> select up
1467 atoms, 1490 bonds, 184 residues, 2 models selected
> color sel hot pink
> color sel deep pink
> select clear
> color #1/E blue
> color #1/F red
> color #1/A cyan
> color #1/C magenta
> color #1/B goldenrod
> color #1/D lime
> select /C:200@OG1
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
161 atoms, 162 bonds, 22 residues, 2 models selected
> select up
4176 atoms, 4256 bonds, 527 residues, 2 models selected
> color (#!1 & sel) lime
> select /D:2@CA
1 atom, 1 residue, 1 model selected
> select /D:8@O
1 atom, 1 residue, 1 model selected
> select up
5 atoms, 4 bonds, 1 residue, 2 models selected
> select up
404 atoms, 404 bonds, 49 residues, 2 models selected
> select up
2757 atoms, 2803 bonds, 346 residues, 2 models selected
> color (#!1 & sel) magenta
> select clear
> close #1
> open
> /Users/shroh/Dropbox/TBC/0_DEG_beta_C/DEGC_beta_extended/DEGC_beta_extended_initial1-coot-3_real_space_refined_016.pdb
Chain information for
DEGC_beta_extended_initial1-coot-3_real_space_refined_016.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
> fetch 1tub
Unknown command: fetch 1tub
> open 1tub fromDatabase pdbe_bio format mmcif
Summary of feedback from opening 1tub fetched from pdbe_bio
---
warning | Missing or incomplete sequence information. Inferred polymer connectivity.
1tub bioassembly 1 title:
Tubulin α-β dimer, electron diffraction [more info...]
Chain information for 1tub bioassembly 1 #2
---
Chain | Description
A | TUBULIN
B | TUBULIN
Non-standard residues in 1tub bioassembly 1 #2
---
GDP — (GDP)
GTP — (GTP)
TXL — (TXL)
Opened 1 biological assemblies for 1tub
Computing secondary structure
> hide atoms
> show cartoons
> ui tool show Matchmaker
> matchmaker #2 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 DEGC_beta_extended_initial1-coot-3_real_space_refined_016.pdb,
chain E (#1) with 1tub bioassembly 1, chain B (#2), sequence alignment score =
1589.7
RMSD between 208 pruned atom pairs is 1.316 angstroms; (across all 427 pairs:
4.886)
Drag select of 304 residues
> select up
4115 atoms, 4173 bonds, 400 residues, 1 model selected
> select up
7351 atoms, 7448 bonds, 631 residues, 1 model selected
> select up
20260 atoms, 20481 bonds, 1458 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 7 residues
> select up
1467 atoms, 1478 bonds, 87 residues, 1 model selected
> select up
8073 atoms, 8152 bonds, 519 residues, 1 model selected
> select down
1467 atoms, 1478 bonds, 87 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 8 residues
> select up
91 atoms, 90 bonds, 13 residues, 1 model selected
> select up
3430 atoms, 3508 bonds, 440 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select ::name="GDP"::name="GTP"::name="TXL"
118 atoms, 127 bonds, 3 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> morph #1,2
Computed 51 frame morph #3
> coordset #3 1,51
> open
> /Users/shroh/Dropbox/TBC/TBCA_betaT_prediction/fold_2024_10_06_11_41_model_0.cif
Chain information for fold_2024_10_06_11_41_model_0.cif #4
---
Chain | Description
A | .
B | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #4 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 DEGC_beta_extended_initial1-coot-3_real_space_refined_016.pdb,
chain E (#1) with fold_2024_10_06_11_41_model_0.cif, chain B (#4), sequence
alignment score = 1811.6
RMSD between 388 pruned atom pairs is 1.014 angstroms; (across all 432 pairs:
2.649)
> open /Users/shroh/Downloads/AF-Q9H4B7-F1-model_v4.pdb
AF-Q9H4B7-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for tubulin β-1 chain (Q9H4B7) [more
info...]
Chain information for AF-Q9H4B7-F1-model_v4.pdb #5
---
Chain | Description | UniProt
A | tubulin β-1 chain | TBB1_HUMAN 1-451
Computing secondary structure
> matchmaker #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 DEGC_beta_extended_initial1-coot-3_real_space_refined_016.pdb,
chain E (#1) with AF-Q9H4B7-F1-model_v4.pdb, chain A (#5), sequence alignment
score = 1911.7
RMSD between 369 pruned atom pairs is 1.076 angstroms; (across all 432 pairs:
2.815)
> open /Users/shroh/Downloads/AF-Q13509-F1-model_v4.pdb
AF-Q13509-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for tubulin β-3 chain (Q13509) [more
info...]
Chain information for AF-Q13509-F1-model_v4.pdb #6
---
Chain | Description | UniProt
A | tubulin β-3 chain | TBB3_HUMAN 1-450
Computing secondary structure
> open /Users/shroh/Downloads/pdb7pjf.ent
pdb7pjf.ent title:
Inhibiting parasite proliferation using A rationally designed ANTI- tubulin
agent [more info...]
Chain information for pdb7pjf.ent #7
---
Chain | Description | UniProt
A | tubulin α-1B chain | TBA1B_HUMAN 1-451
B | tubulin β-3 chain | TBB3_HUMAN 1-460
F | designed ankyrin repeat protein (darpin) D1 |
Non-standard residues in pdb7pjf.ent #7
---
GTP — guanosine-5'-triphosphate
MG — magnesium ion
30 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> matchmaker #6#!7 to #1
Computing secondary structure
[Repeated 2 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 DEGC_beta_extended_initial1-coot-3_real_space_refined_016.pdb,
chain E (#1) with AF-Q13509-F1-model_v4.pdb, chain A (#6), sequence alignment
score = 1787.8
RMSD between 375 pruned atom pairs is 1.062 angstroms; (across all 432 pairs:
2.843)
Matchmaker DEGC_beta_extended_initial1-coot-3_real_space_refined_016.pdb,
chain E (#1) with pdb7pjf.ent, chain B (#7), sequence alignment score = 1822.6
RMSD between 381 pruned atom pairs is 0.987 angstroms; (across all 428 pairs:
2.614)
> hide #3 models
> show #3 models
> hide #4 models
> hide #5 models
> hide #6 models
> close #2
> close #3
Drag select of 14 residues
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select up
176 atoms, 176 bonds, 22 residues, 1 model selected
> select up
1135 atoms, 1150 bonds, 155 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 223 residues, 3 pseudobonds
> select up
2507 atoms, 2553 bonds, 3 pseudobonds, 325 residues, 2 models selected
> select up
3251 atoms, 3323 bonds, 3 pseudobonds, 419 residues, 2 models selected
> delete atoms (#!7 & sel)
> delete bonds (#!7 & sel)
Drag select of 8 atoms, 10 bonds
> select up
10 atoms, 10 bonds, 1 residue, 1 model selected
> select up
32 atoms, 34 bonds, 1 residue, 1 model selected
> select up
227 atoms, 34 bonds, 196 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #1 models
> show #4 models
> hide #4 models
> show #5 models
> hide #5 models
> show #6 models
> hide #6 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> close #4-6
> select ::name="GTP"::name="HOH"::name="MG"
277 atoms, 34 bonds, 6 pseudobonds, 246 residues, 2 models selected
> delete atoms (#!7 & sel)
> delete bonds (#!7 & sel)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> morph #1,7
Computed 51 frame morph #2
> coordset #2 1,51
> open /Users/shroh/Downloads/pdb7pjf.ent format pdb
pdb7pjf.ent title:
Inhibiting parasite proliferation using A rationally designed ANTI- tubulin
agent [more info...]
Chain information for pdb7pjf.ent #3
---
Chain | Description | UniProt
A | tubulin α-1B chain | TBA1B_HUMAN 1-451
B | tubulin β-3 chain | TBB3_HUMAN 1-460
F | designed ankyrin repeat protein (darpin) D1 |
Non-standard residues in pdb7pjf.ent #3
---
GTP — guanosine-5'-triphosphate
MG — magnesium ion
30 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> matchmaker #!7 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 DEGC_beta_extended_initial1-coot-3_real_space_refined_016.pdb,
chain E (#1) with pdb7pjf.ent, chain B (#7), sequence alignment score = 1822.6
RMSD between 381 pruned atom pairs is 0.987 angstroms; (across all 428 pairs:
2.614)
> matchmaker #!7 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 DEGC_beta_extended_initial1-coot-3_real_space_refined_016.pdb,
chain E (#1) with pdb7pjf.ent, chain B (#7), sequence alignment score = 1822.6
RMSD between 381 pruned atom pairs is 0.987 angstroms; (across all 428 pairs:
2.614)
> matchmaker #!3 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 DEGC_beta_extended_initial1-coot-3_real_space_refined_016.pdb,
chain E (#1) with pdb7pjf.ent, chain B (#3), sequence alignment score = 1822.6
RMSD between 381 pruned atom pairs is 0.987 angstroms; (across all 428 pairs:
2.614)
Drag select of 26 residues
> select up
413 atoms, 416 bonds, 56 residues, 1 model selected
> select up
1135 atoms, 1150 bonds, 155 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!7 models
> hide #!7 models
> open
> /Users/shroh/Dropbox/TBC/0_DEG_abTub/tbcdeg_ab_initial_real_space_refined_012-coot-0.pdb
Summary of feedback from opening
/Users/shroh/Dropbox/TBC/0_DEG_abTub/tbcdeg_ab_initial_real_space_refined_012-coot-0.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 31 VAL A 46 1 16
Start residue of secondary structure not found: HELIX 2 2 GLY A 50 TYR A 67 1
18
Start residue of secondary structure not found: HELIX 3 3 PRO A 71 GLN A 90 1
20
Start residue of secondary structure not found: HELIX 4 4 ALA A 96 ARG A 113 1
18
Start residue of secondary structure not found: HELIX 5 5 TYR A 115 ARG A 120
1 6
91 messages similar to the above omitted
End residue of secondary structure not found: HELIX 97 97 PRO E 72 THR E 80 1
9
Start residue of secondary structure not found: HELIX 98 98 PRO E 89 GLN E 91
1 3
Start residue of secondary structure not found: HELIX 99 99 TYR E 103 GLN E
128 1 26
Start residue of secondary structure not found: HELIX 100 100 GLY E 144 ASP E
160 1 17
Start residue of secondary structure not found: HELIX 101 101 GLU E 183 THR E
194 1 12
Start residue of secondary structure not found: HELIX 102 102 ASN E 206 ASN E
216 1 11
5 messages similar to the above omitted
End residue of secondary structure not found: HELIX 108 108 PRO E 307 HIS E
309 1 3
Start residue of secondary structure not found: HELIX 109 109 PRO E 325 LYS E
338 1 14
Start residue of secondary structure not found: HELIX 110 110 THR E 382 LYS E
401 1 20
Start residue of secondary structure not found: HELIX 111 111 VAL E 405 TRP E
407 1 3
Start residue of secondary structure not found: HELIX 112 112 VAL E 409 GLU E
411 1 3
Start residue of secondary structure not found: HELIX 113 113 GLU E 415 GLY E
436 1 22
77 messages similar to the above omitted
Chain information for tbcdeg_ab_initial_real_space_refined_012-coot-0.pdb #4
---
Chain | Description
D | No description available
E | No description available
G | No description available
a | No description available
b | No description available
> matchmaker #4 to #1
Computing secondary structure
[Repeated 2 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 DEGC_beta_extended_initial1-coot-3_real_space_refined_016.pdb,
chain E (#1) with tbcdeg_ab_initial_real_space_refined_012-coot-0.pdb, chain b
(#4), sequence alignment score = 1767.8
RMSD between 396 pruned atom pairs is 0.687 angstroms; (across all 432 pairs:
2.426)
> hide #4#!2-3 atoms
> show #4#!2-3 cartoons
> hide #!2 models
> hide #!3 models
> show #1 models
> open /Users/shroh/Dropbox/TBC/0_DEG_abTub/tbc_deg_alphabeta_deep.mrc
Opened tbc_deg_alphabeta_deep.mrc as #5, grid size 200,200,200, pixel 1.41,
shown at level 0.0563, step 1, values float32
> close #5
> show #!2 models
> hide #4 models
> hide #1 models
> select #2/E:335
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
118 atoms, 121 bonds, 15 residues, 1 model selected
> color sel red
> hide #!2 models
> show #4 models
> select #4/b:339
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
231 atoms, 235 bonds, 14 residues, 1 model selected
> color sel red
> show #!2 models
> show #!3 models
> hide #!3 models
> show #!7 models
> hide #!7 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 #!2 models
> hide #!3 models
> hide #4 models
> show #!3 models
> select ::name="GTP"::name="HOH"::name="MG"
504 atoms, 68 bonds, 10 pseudobonds, 442 residues, 2 models selected
> delete atoms (#!3 & sel)
> delete bonds (#!3 & sel)
> open /Users/shroh/Downloads/AF-P02554-F1-model_v4.pdb
AF-P02554-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for tubulin β chain (P02554) [more info...]
Chain information for AF-P02554-F1-model_v4.pdb #5
---
Chain | Description | UniProt
A | tubulin β chain | TBB_PIG 1-445
Computing secondary structure
> matchmaker #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 DEGC_beta_extended_initial1-coot-3_real_space_refined_016.pdb,
chain E (#1) with AF-P02554-F1-model_v4.pdb, chain A (#5), sequence alignment
score = 1795.9
RMSD between 371 pruned atom pairs is 1.087 angstroms; (across all 432 pairs:
2.866)
> hide #!3 models
> hide #5 models
> show #1 models
> show #5 models
> hide #5 models
> show #5 models
> show #!7 models
> hide #5 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #4 models
> hide #4 models
> show #5 models
> hide #5 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #5 models
> close #5
> show #!3 models
> open /Users/shroh/Downloads/pdb7pjf.ent format pdb
pdb7pjf.ent title:
Inhibiting parasite proliferation using A rationally designed ANTI- tubulin
agent [more info...]
Chain information for pdb7pjf.ent #5
---
Chain | Description | UniProt
A | tubulin α-1B chain | TBA1B_HUMAN 1-451
B | tubulin β-3 chain | TBB3_HUMAN 1-460
F | designed ankyrin repeat protein (darpin) D1 |
Non-standard residues in pdb7pjf.ent #5
---
GTP — guanosine-5'-triphosphate
MG — magnesium ion
30 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> matchmaker #!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 DEGC_beta_extended_initial1-coot-3_real_space_refined_016.pdb,
chain E (#1) with pdb7pjf.ent, chain B (#5), sequence alignment score = 1822.6
RMSD between 381 pruned atom pairs is 0.987 angstroms; (across all 428 pairs:
2.614)
Drag select of 23 residues
> select up
423 atoms, 423 bonds, 59 residues, 1 model selected
> select up
1135 atoms, 1150 bonds, 155 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select ::name="GTP"::name="HOH"::name="MG"
504 atoms, 68 bonds, 10 pseudobonds, 442 residues, 2 models selected
> delete atoms (#!5 & sel)
> delete bonds (#!5 & sel)
> show #4 models
> hide #4 models
> open
> /Users/shroh/Dropbox/TBC/0_DEG_abTub/tbcdeg_ab_initial_real_space_refined_012-coot-0.pdb
Summary of feedback from opening
/Users/shroh/Dropbox/TBC/0_DEG_abTub/tbcdeg_ab_initial_real_space_refined_012-coot-0.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 31 VAL A 46 1 16
Start residue of secondary structure not found: HELIX 2 2 GLY A 50 TYR A 67 1
18
Start residue of secondary structure not found: HELIX 3 3 PRO A 71 GLN A 90 1
20
Start residue of secondary structure not found: HELIX 4 4 ALA A 96 ARG A 113 1
18
Start residue of secondary structure not found: HELIX 5 5 TYR A 115 ARG A 120
1 6
91 messages similar to the above omitted
End residue of secondary structure not found: HELIX 97 97 PRO E 72 THR E 80 1
9
Start residue of secondary structure not found: HELIX 98 98 PRO E 89 GLN E 91
1 3
Start residue of secondary structure not found: HELIX 99 99 TYR E 103 GLN E
128 1 26
Start residue of secondary structure not found: HELIX 100 100 GLY E 144 ASP E
160 1 17
Start residue of secondary structure not found: HELIX 101 101 GLU E 183 THR E
194 1 12
Start residue of secondary structure not found: HELIX 102 102 ASN E 206 ASN E
216 1 11
5 messages similar to the above omitted
End residue of secondary structure not found: HELIX 108 108 PRO E 307 HIS E
309 1 3
Start residue of secondary structure not found: HELIX 109 109 PRO E 325 LYS E
338 1 14
Start residue of secondary structure not found: HELIX 110 110 THR E 382 LYS E
401 1 20
Start residue of secondary structure not found: HELIX 111 111 VAL E 405 TRP E
407 1 3
Start residue of secondary structure not found: HELIX 112 112 VAL E 409 GLU E
411 1 3
Start residue of secondary structure not found: HELIX 113 113 GLU E 415 GLY E
436 1 22
77 messages similar to the above omitted
Chain information for tbcdeg_ab_initial_real_space_refined_012-coot-0.pdb #6
---
Chain | Description
D | No description available
E | No description available
G | No description available
a | No description available
b | No description available
> matchmaker #6 to #1
Computing secondary structure
[Repeated 2 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 DEGC_beta_extended_initial1-coot-3_real_space_refined_016.pdb,
chain E (#1) with tbcdeg_ab_initial_real_space_refined_012-coot-0.pdb, chain b
(#6), sequence alignment score = 1767.8
RMSD between 396 pruned atom pairs is 0.687 angstroms; (across all 432 pairs:
2.426)
> hide #1,6#!3,5 atoms
> show #1,6#!3,5 cartoons
Drag select of 9 residues
> select up
210 atoms, 210 bonds, 16 residues, 1 model selected
> select up
6933 atoms, 7012 bonds, 451 residues, 1 model selected
> select ~sel & ##selected
36901 atoms, 37261 bonds, 2347 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #6 models
> show #6 models
> hide #!5 models
> hide #!3 models
> hide #1 models
> show #!2 models
> show #!7 models
> hide #!7 models
> show #!5 models
Drag select of 1 residues
> select up
51 atoms, 50 bonds, 8 residues, 1 model selected
> select up
2292 atoms, 2342 bonds, 295 residues, 1 model selected
> select ~sel & ##selected
4301 atoms, 4396 bonds, 3 pseudobonds, 552 residues, 2 models selected
> delete atoms (#!5 & sel)
> delete bonds (#!5 & sel)
> hide #6 models
> hide #!5 models
> show #!3 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> hide #!3 models
> hide #!2 models
> show #!7 models
> hide #!7 models
> show #!5 models
> show #6 models
> hide #!5 models
> hide #6 models
> morph #5,6
Computed 51 frame morph #8
> coordset #8 1,51
> show #!7 models
> hide #!7 models
> show #!3 models
> hide #!3 models
> close #8
> show #6 models
> show #!5 models
> close #5
> open /Users/shroh/Downloads/pdb7pjf.ent format pdb
pdb7pjf.ent title:
Inhibiting parasite proliferation using A rationally designed ANTI- tubulin
agent [more info...]
Chain information for pdb7pjf.ent #5
---
Chain | Description | UniProt
A | tubulin α-1B chain | TBA1B_HUMAN 1-451
B | tubulin β-3 chain | TBB3_HUMAN 1-460
F | designed ankyrin repeat protein (darpin) D1 |
Non-standard residues in pdb7pjf.ent #5
---
GTP — guanosine-5'-triphosphate
MG — magnesium ion
30 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> matchmaker #!7 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 DEGC_beta_extended_initial1-coot-3_real_space_refined_016.pdb,
chain E (#1) with pdb7pjf.ent, chain B (#7), sequence alignment score = 1822.6
RMSD between 381 pruned atom pairs is 0.987 angstroms; (across all 428 pairs:
2.614)
> matchmaker #!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 DEGC_beta_extended_initial1-coot-3_real_space_refined_016.pdb,
chain E (#1) with pdb7pjf.ent, chain B (#5), sequence alignment score = 1822.6
RMSD between 381 pruned atom pairs is 0.987 angstroms; (across all 428 pairs:
2.614)
Drag select of 82 atoms, 262 residues, 6 pseudobonds, 63 bonds
> select up
1997 atoms, 2009 bonds, 6 pseudobonds, 278 residues, 2 models selected
> select up
2006 atoms, 2020 bonds, 6 pseudobonds, 278 residues, 2 models selected
> select up
2965 atoms, 2998 bonds, 6 pseudobonds, 399 residues, 2 models selected
> select up
4523 atoms, 4599 bonds, 6 pseudobonds, 598 residues, 2 models selected
> select up
4754 atoms, 4599 bonds, 6 pseudobonds, 829 residues, 2 models selected
> select up
8232 atoms, 7956 bonds, 10 pseudobonds, 1444 residues, 2 models selected
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select down
4754 atoms, 4599 bonds, 6 pseudobonds, 829 residues, 2 models selected
> delete atoms (#!5 & sel)
> delete bonds (#!5 & sel)
> select ::name="GTP"::name="HOH"::name="MG"
227 atoms, 34 bonds, 4 pseudobonds, 196 residues, 2 models selected
> delete atoms (#!5 & sel)
> delete bonds (#!5 & sel)
> morph #5,6
Computed 51 frame morph #8
> coordset #8 1,51
> show #6 models
> hide #6 models
> show #!3 models
> hide #!3 models
> show #!2 models
> show #!5 models
> hide #!5 models
> open
> /Users/shroh/Dropbox/TBC/TBCA_betaT_prediction/fold_2024_10_06_11_41_model_0.cif
Chain information for fold_2024_10_06_11_41_model_0.cif #9
---
Chain | Description
A | .
B | .
Computing secondary structure
> matchmaker #9 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 DEGC_beta_extended_initial1-coot-3_real_space_refined_016.pdb,
chain E (#1) with fold_2024_10_06_11_41_model_0.cif, chain B (#9), sequence
alignment score = 1811.6
RMSD between 388 pruned atom pairs is 1.014 angstroms; (across all 432 pairs:
2.649)
> hide #!8 models
Drag select of 20 residues
> select up
321 atoms, 323 bonds, 38 residues, 1 model selected
> show sel target ab
Drag select of 4 residues
> select up
190 atoms, 196 bonds, 23 residues, 2 models selected
> show sel target ab
> style sel stick
Changed 190 atom styles
> color sel byelement
> hide #9 models
> show #!8 models
> select #8/A:175
7 atoms, 7 bonds, 1 residue, 1 model selected
> select add #8/A:179
14 atoms, 13 bonds, 2 residues, 1 model selected
> select add #8/A:182
21 atoms, 19 bonds, 3 residues, 1 model selected
> select add #8/A:404
32 atoms, 30 bonds, 4 residues, 1 model selected
> select add #8/A:403
37 atoms, 34 bonds, 5 residues, 1 model selected
> select add #8/A:394
46 atoms, 42 bonds, 6 residues, 1 model selected
> select up
398 atoms, 410 bonds, 49 residues, 1 model selected
> style sel stick
Changed 398 atom styles
> color sel byelement
> show sel atoms
> select #2/E:252
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #2/E:350
18 atoms, 16 bonds, 2 residues, 1 model selected
> select up
103 atoms, 101 bonds, 14 residues, 1 model selected
> show sel target ab
> style sel stick
Changed 103 atom styles
> select clear
> hide #!8 models
> hide #!2 models
> show #1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #4 models
> hide #4 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!7 models
> hide #!7 models
> show #!5 models
> hide #!5 models
> open /Users/shroh/Downloads/pdb7pjf.ent format pdb
pdb7pjf.ent title:
Inhibiting parasite proliferation using A rationally designed ANTI- tubulin
agent [more info...]
Chain information for pdb7pjf.ent #10
---
Chain | Description | UniProt
A | tubulin α-1B chain | TBA1B_HUMAN 1-451
B | tubulin β-3 chain | TBB3_HUMAN 1-460
F | designed ankyrin repeat protein (darpin) D1 |
Non-standard residues in pdb7pjf.ent #10
---
GTP — guanosine-5'-triphosphate
MG — magnesium ion
30 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> matchmaker #!10 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 DEGC_beta_extended_initial1-coot-3_real_space_refined_016.pdb,
chain E (#1) with pdb7pjf.ent, chain B (#10), sequence alignment score =
1822.6
RMSD between 381 pruned atom pairs is 0.987 angstroms; (across all 428 pairs:
2.614)
> hide #1 models
> select ::name="GTP"::name="HOH"::name="MG"
504 atoms, 68 bonds, 10 pseudobonds, 442 residues, 2 models selected
> delete atoms (#!10 & sel)
> delete bonds (#!10 & sel)
Drag select of 21 residues
> select up
350 atoms, 354 bonds, 46 residues, 1 model selected
> select up
1135 atoms, 1150 bonds, 155 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select clear
Drag select of 128 atoms, 847 residues, 4 pseudobonds, 103 bonds
> save /Users/shroh/Dropbox/TBC/interface_alpha_beta_pisa.cxs
——— End of log from Thu Oct 24 14:16:16 2024 ———
opened ChimeraX session
> show #!8 models
> hide #!10 models
> hide #!8 models
> show #!2 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!2 models
> show #!2 models
> show #!10 models
> hide #!10 models
> show #9 models
> show #!8 models
> show #!7 models
> show #6 models
> show #4 models
> show #!3 models
> show #1 models
> show #!10 models
> hide #!2 models
> hide #!3 models
> hide #4 models
> hide #!5 models
> hide #6 models
> hide #!7 models
> hide #!8 models
> hide #9 models
> hide #!10 models
> show #!10 models
> show #9 models
> show #!8 models
> show #!7 models
> show #6 models
> show #!5 models
> show #4 models
> show #!3 models
> show #!2 models
> hide #1 models
> hide #!3 models
> hide #4 models
> hide #!5 models
> hide #6 models
> hide #!8 models
> hide #!7 models
> show #!8 models
> hide #9 models
> hide #!10 models
Drag select of 72 atoms, 320 residues, 3 pseudobonds, 61 bonds
> select up
2492 atoms, 2535 bonds, 3 pseudobonds, 321 residues, 2 models selected
> select up
2496 atoms, 2539 bonds, 3 pseudobonds, 321 residues, 2 models selected
> select up
2827 atoms, 2882 bonds, 3 pseudobonds, 365 residues, 2 models selected
> select up
3248 atoms, 3320 bonds, 3 pseudobonds, 419 residues, 2 models selected
> ui tool show "Color Actions"
> color sel green
Drag select of 201 residues
> select #2/E:343
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
118 atoms, 121 bonds, 15 residues, 1 model selected
> select ~sel & ##selected
3051 atoms, 3109 bonds, 1 pseudobond, 413 residues, 2 models selected
> color sel indigo
> select clear
> select #2/E:346
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
118 atoms, 121 bonds, 15 residues, 1 model selected
> hide #3.1 models
> hide #!3.2 models
> hide #2.1 models
> hide #!5.2 models
> hide #8.1 models
> hide #!8.2 models
> select clear
> select #2/E:346
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
118 atoms, 121 bonds, 15 residues, 1 model selected
> open
> /Users/shroh/Dropbox/TBC/0_DEG_C_abTub_GTP/DEG_C_abTub_GTPAlFx/CDG_abTub_alfx_class2_NCterm-C/initial2-coot-0_isolde3_real_space_refined_022.pdb
> format pdb
Chain information for initial2-coot-0_isolde3_real_space_refined_022.pdb #11
---
Chain | Description
C | No description available
D | No description available
G | No description available
a | No description available
b | No description available
> ui tool show Matchmaker
> hide #!2 models
> matchmaker #11 to #1/E pairing bs
Computing secondary structure
Parameters
---
Chain pairing | bs
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 DEGC_beta_extended_initial1-coot-3_real_space_refined_016.pdb,
chain E (#1) with initial2-coot-0_isolde3_real_space_refined_022.pdb, chain b
(#11), sequence alignment score = 2083.8
RMSD between 392 pruned atom pairs is 0.859 angstroms; (across all 432 pairs:
2.520)
> select clear
> hide #5.1 models
> hide #!8 models
> hide #11 atoms
> show #11 cartoons
> select clear
[Repeated 1 time(s)]
> show #!3 models
> hide #11 models
> select clear
> open 7pjf fromDatabase pdb format mmcif
7pjf title:
Inhibiting parasite proliferation using a rationally designed anti-tubulin
agent [more info...]
Chain information for 7pjf #12
---
Chain | Description | UniProt
A | Tubulin alpha-1B chain | TBA1B_HUMAN 1-451
B | Tubulin beta-3 chain | TBB3_HUMAN 1-460
F | Designed ankyrin repeat protein (DARPIN) D1 |
Non-standard residues in 7pjf #12
---
GTP — guanosine-5'-triphosphate
MG — magnesium ion
30 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> matchmaker #!12 to #1/E pairing bs
Computing secondary structure
Parameters
---
Chain pairing | bs
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 DEGC_beta_extended_initial1-coot-3_real_space_refined_016.pdb,
chain E (#1) with 7pjf, chain B (#12), sequence alignment score = 1822.6
RMSD between 381 pruned atom pairs is 0.987 angstroms; (across all 428 pairs:
2.614)
Drag select of 44 residues
> select up
601 atoms, 604 bonds, 82 residues, 1 model selected
> select up
1135 atoms, 1150 bonds, 155 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select clear
> show #1 models
> show #!2 models
> show #4 models
> show #!5 models
> show #6 models
> show #!7 models
> show #!8 models
> show #9 models
> show #!10 models
> show #11 models
> open
> /Users/shroh/Dropbox/TBC/0_DEG_C_abTub_GTP/DEG_C_abTub_GTPAlFx/CDG_abTub_alfx_class2_NCterm-C/initial2-coot-0_isolde4.pdb
> format pdb
Chain information for initial2-coot-0_isolde4.pdb #13
---
Chain | Description
C | No description available
D | No description available
G | No description available
a | No description available
b | No description available
> hide #11 models
> show #11 models
> hide #11 models
> show #11 models
> hide #13 models
> show #13 models
> open
> /Users/shroh/Dropbox/TBC/1_DEG_beta_C/DEGC_beta_closed/DEGC_beta_closed.pdb
Chain information for DEGC_beta_closed.pdb #14
---
Chain | Description
A | No description available
C | No description available
D | No description available
E | No description available
> open
> /Users/shroh/Dropbox/TBC/4_DEG_abTub/tbcdeg_ab_initial_real_space_refined_initial_GTP2.pdb
Chain information for tbcdeg_ab_initial_real_space_refined_initial_GTP2.pdb
#15
---
Chain | Description
A | No description available
D | No description available
E | No description available
a | No description available
b | No description available
> open /Users/shroh/Dropbox/TBC/4_DEG_abTub/DEG(e)C_abTub_GTP_241114_2.pdb
Chain information for DEG(e)C_abTub_GTP_241114_2.pdb #16
---
Chain | Description
C | No description available
D | No description available
E | No description available
a | No description available
b | No description available
> open /Users/shroh/Dropbox/TBC/4_DEG_abTub/DEG(e)C_abTub_GTP_241114.pdb
Chain information for DEG(e)C_abTub_GTP_241114.pdb #17
---
Chain | Description
C | No description available
D | No description available
E | No description available
a | No description available
b | No description available
> close #1,4,6,9,11,13-17#2-3,5,7-8,10,12
> open /Users/shroh/Dropbox/TBC/0_Model_pool/Z_7pjf.pdb
Chain information for Z_7pjf.pdb #1
---
Chain | Description
A | No description available
B | No description available
F | No description available
30 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open
> /Users/shroh/Dropbox/TBC/0_Model_pool/1_DG(c)_bTub_GTP_real_space_refined_1.pdb
Chain information for 1_DG(c)_bTub_GTP_real_space_refined_1.pdb #2
---
Chain | Description
D | No description available
G | No description available
b | No description available
> open /Users/shroh/Dropbox/TBC/0_Model_pool/2_DEG(c)_bTub_GTP_241017.pdb
Chain information for 2_DEG(c)_bTub_GTP_241017.pdb #3
---
Chain | Description
D | No description available
E | No description available
G | No description available
b | No description available
> open /Users/shroh/Dropbox/TBC/0_Model_pool/3_DEG(e)C_bTub_GTP_241017.pdb
Chain information for 3_DEG(e)C_bTub_GTP_241017.pdb #4
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
> open /Users/shroh/Dropbox/TBC/0_Model_pool/4_DEG(e)C_abTub_GTP_241114.pdb
Chain information for 4_DEG(e)C_abTub_GTP_241114.pdb #5
---
Chain | Description
C | No description available
D | No description available
E | No description available
a | No description available
b | No description available
> open /Users/shroh/Dropbox/TBC/0_Model_pool/5_DEG(e)C(C)_abTub_GTP_241114.pdb
Chain information for 5_DEG(e)C(C)_abTub_GTP_241114.pdb #6
---
Chain | Description
C | No description available
D | No description available
E | No description available
G | No description available
a | No description available
b | No description available
> open
> /Users/shroh/Dropbox/TBC/0_Model_pool/6_DEG(e)C(NC)_abTub_GTP_241114.pdb
Chain information for 6_DEG(e)C(NC)_abTub_GTP_241114.pdb #7
---
Chain | Description
C | No description available
D | No description available
G | No description available
a | No description available
b | No description available
> select clear
> hide atoms
> show cartoons
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #4-6#!1-3 to #7/b pairing bs
Computing secondary structure
[Repeated 6 time(s)] Parameters
---
Chain pairing | bs
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 6_DEG(e)C(NC)_abTub_GTP_241114.pdb, chain b (#7) with
3_DEG(e)C_bTub_GTP_241017.pdb, chain E (#4), sequence alignment score = 2083.8
RMSD between 392 pruned atom pairs is 0.859 angstroms; (across all 432 pairs:
2.520)
Matchmaker 6_DEG(e)C(NC)_abTub_GTP_241114.pdb, chain b (#7) with
4_DEG(e)C_abTub_GTP_241114.pdb, chain b (#5), sequence alignment score =
2183.4
RMSD between 404 pruned atom pairs is 0.611 angstroms; (across all 432 pairs:
2.207)
Matchmaker 6_DEG(e)C(NC)_abTub_GTP_241114.pdb, chain b (#7) with
5_DEG(e)C(C)_abTub_GTP_241114.pdb, chain b (#6), sequence alignment score =
2178
RMSD between 395 pruned atom pairs is 0.701 angstroms; (across all 432 pairs:
1.904)
Matchmaker 6_DEG(e)C(NC)_abTub_GTP_241114.pdb, chain b (#7) with Z_7pjf.pdb,
chain B (#1), sequence alignment score = 1952.8
RMSD between 418 pruned atom pairs is 0.764 angstroms; (across all 428 pairs:
0.971)
Matchmaker 6_DEG(e)C(NC)_abTub_GTP_241114.pdb, chain b (#7) with
1_DG(c)_bTub_GTP_real_space_refined_1.pdb, chain b (#2), sequence alignment
score = 2178
RMSD between 402 pruned atom pairs is 0.694 angstroms; (across all 432 pairs:
2.406)
Matchmaker 6_DEG(e)C(NC)_abTub_GTP_241114.pdb, chain b (#7) with
2_DEG(c)_bTub_GTP_241017.pdb, chain b (#3), sequence alignment score = 2164.8
RMSD between 402 pruned atom pairs is 0.710 angstroms; (across all 432 pairs:
2.435)
> color #4/a forest green
> color #4/b indigo
> color #4/D cyan
> color #4/E dodger blue
> color #4/G dark orange
> color #4/C hot pink
> color #4/J yellow
> color #4/H yellow
> color #4/I yellow
> color #2/a forest green
> color #2/b indigo
> color #2/D cyan
> color #2/E dodger blue
> color #2/G dark orange
> color #2/C hot pink
> color #2/J yellow
> color #2/H yellow
> color #2/I yellow
> color #3/a forest green
> color #3/b indigo
> color #3/D cyan
> color #3/E dodger blue
> color #3/G dark orange
> color #32/C hot pink
> color #3/J yellow
> color #3/H yellow
> color #3/I yellow
> color #5/a forest green
> color #5/b indigo
> color #5/D cyan
> color #5/E dodger blue
> color #5/G dark orange
> color #32/5 hot pink
> color #5/J yellow
> color #5/H yellow
> color #5/I yellow
> color #6,7/a forest green
> color #5/b indigo
> color #5/D cyan
> color #5/E dodger blue
> color #5/G dark orange
> color #32/5 hot pink
> color #5/J yellow
> color #5/H yellow
> color #5/I yellow
> color #6,7/a forest green
> color #6,7/b indigo
> color #6,7/D cyan
> color #5/E dodger blue
> color #5/G dark orange
> color #32/5 hot pink
> color #5/J yellow
> color #5/H yellow
> color #5/I yellow
> color #6,7/a forest green
> color #6,7/b indigo
> color #6,7/D cyan
> color #6,7/E dodger blue
> color #6,7/G dark orange
> color #5,6,7/C hot pink
> color #5,6,7/J yellow
> color #5,6,7/H yellow
> color #5,6,7/I yellow
> color #2,3,4,5,6,7/a forest green
> color #2,3,4,5,6,7/b indigo
> color #2,3,4,5,6,7/D cyan
> color #2,3,4,5,6,7/E dodger blue
> color #2,3,4,5,6,7/G dark orange
> color #2,3,4,5,6,7/C hot pink
> color #2,3,4,5,6,7/J yellow
> color #2,3,4,5,6,7/H yellow
> color #2,3,4,5,6,7/I yellow
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #5 models
> hide #6 models
> hide #7 models
> open
> /Users/shroh/Dropbox/TBC/3_DEG_beta_C/DEGC_beta_extended/DEG(e)C_bTub_GTP_241017.pdb
Summary of feedback from opening
/Users/shroh/Dropbox/TBC/3_DEG_beta_C/DEGC_beta_extended/DEG(e)C_bTub_GTP_241017.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO D 180 TRP D 182 1 3
Start residue of secondary structure not found: HELIX 2 2 ALA D 198 LEU D 201
1 4
Start residue of secondary structure not found: HELIX 3 3 ILE D 299 SER D 306
1 8
Start residue of secondary structure not found: HELIX 4 4 GLU D 338 GLU D 340
1 3
Start residue of secondary structure not found: HELIX 5 5 GLY C 31 VAL C 46 1
16
93 messages similar to the above omitted
End residue of secondary structure not found: SHEET 3 3 3 ASP D 205 THR D 209
0
Start residue of secondary structure not found: SHEET 4 4 4 THR D 215 LEU D
218 0
Start residue of secondary structure not found: SHEET 5 5 5 THR D 224 THR D
228 0
Start residue of secondary structure not found: SHEET 6 6 6 LYS D 234 CYS D
237 0
Start residue of secondary structure not found: SHEET 7 7 7 SER D 243 GLU D
247 0
Start residue of secondary structure not found: SHEET 8 8 8 VAL D 253 CYS D
258 0
26 messages similar to the above omitted
Chain information for DEG(e)C_bTub_GTP_241017.pdb #8
---
Chain | Description
C | No description available
D | No description available
E | No description available
G | No description available
b | No description available
> matchmaker #8 to #7/b pairing bs
Computing secondary structure
[Repeated 2 time(s)] Parameters
---
Chain pairing | bs
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 6_DEG(e)C(NC)_abTub_GTP_241114.pdb, chain b (#7) with
DEG(e)C_bTub_GTP_241017.pdb, chain b (#8), sequence alignment score = 2083.8
RMSD between 392 pruned atom pairs is 0.859 angstroms; (across all 432 pairs:
2.520)
> hide #4,8 atoms
> show #4,8 cartoons
> close #4
> close #8
> open
> /Users/shroh/Dropbox/TBC/3_DEG_beta_C/DEGC_beta_extended/DEG(e)C_bTub_GTP_241017.pdb
Summary of feedback from opening
/Users/shroh/Dropbox/TBC/3_DEG_beta_C/DEGC_beta_extended/DEG(e)C_bTub_GTP_241017.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO D 180 TRP D 182 1 3
Start residue of secondary structure not found: HELIX 2 2 ALA D 198 LEU D 201
1 4
Start residue of secondary structure not found: HELIX 3 3 ILE D 299 SER D 306
1 8
Start residue of secondary structure not found: HELIX 4 4 GLU D 338 GLU D 340
1 3
Start residue of secondary structure not found: HELIX 5 5 GLY C 31 VAL C 46 1
16
93 messages similar to the above omitted
End residue of secondary structure not found: SHEET 3 3 3 ASP D 205 THR D 209
0
Start residue of secondary structure not found: SHEET 4 4 4 THR D 215 LEU D
218 0
Start residue of secondary structure not found: SHEET 5 5 5 THR D 224 THR D
228 0
Start residue of secondary structure not found: SHEET 6 6 6 LYS D 234 CYS D
237 0
Start residue of secondary structure not found: SHEET 7 7 7 SER D 243 GLU D
247 0
Start residue of secondary structure not found: SHEET 8 8 8 VAL D 253 CYS D
258 0
26 messages similar to the above omitted
Chain information for DEG(e)C_bTub_GTP_241017.pdb #4
---
Chain | Description
C | No description available
D | No description available
E | No description available
G | No description available
b | No description available
> matchmaker #4 to #7/b pairing bs
Computing secondary structure
[Repeated 2 time(s)] Parameters
---
Chain pairing | bs
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 6_DEG(e)C(NC)_abTub_GTP_241114.pdb, chain b (#7) with
DEG(e)C_bTub_GTP_241017.pdb, chain b (#4), sequence alignment score = 2083.8
RMSD between 392 pruned atom pairs is 0.859 angstroms; (across all 432 pairs:
2.520)
> hide #4 atoms
> show #4 cartoons
> color #2,3,4,5,6,7/a forest green
> color #2,3,4,5,6,7/b indigo
> color #2,3,4,5,6,7/D cyan
> color #2,3,4,5,6,7/E dodger blue
> color #2,3,4,5,6,7/G dark orange
> color #2,3,4,5,6,7/C hot pink
> color #2,3,4,5,6,7/J yellow
> color #2,3,4,5,6,7/H yellow
> color #2,3,4,5,6,7/I yellow
> hide #4 models
> show #!1 models
Drag select of 38 residues
> select up
492 atoms, 495 bonds, 68 residues, 1 model selected
> select up
1135 atoms, 1150 bonds, 155 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 52 residues
> select up
1002 atoms, 1017 bonds, 127 residues, 1 model selected
> select up
2917 atoms, 2982 bonds, 374 residues, 1 model selected
> ui tool show "Color Actions"
> color sel indigo
Drag select of 79 residues, 2 pseudobonds
> select up
791 atoms, 802 bonds, 2 pseudobonds, 107 residues, 2 models selected
> select up
2983 atoms, 3049 bonds, 2 pseudobonds, 383 residues, 2 models selected
> color sel forest green
> select #1/B:11
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
148 atoms, 151 bonds, 19 residues, 1 model selected
> select up
425 atoms, 433 bonds, 54 residues, 1 model selected
> select clear
Drag select of 4 residues
> select up
161 atoms, 163 bonds, 18 residues, 1 model selected
> select up
2917 atoms, 2982 bonds, 374 residues, 1 model selected
> select up
2922 atoms, 2986 bonds, 375 residues, 1 model selected
> select up
3342 atoms, 3415 bonds, 428 residues, 1 model selected
> color sel indigo
Drag select of 284 residues, 3 pseudobonds
> select up
2879 atoms, 2932 bonds, 3 pseudobonds, 371 residues, 2 models selected
> select up
3251 atoms, 3323 bonds, 3 pseudobonds, 419 residues, 2 models selected
> select up
3478 atoms, 3357 bonds, 3 pseudobonds, 615 residues, 2 models selected
> select up
7097 atoms, 6806 bonds, 4 pseudobonds, 1289 residues, 2 models selected
> select down
3478 atoms, 3357 bonds, 3 pseudobonds, 615 residues, 2 models selected
> select down
3251 atoms, 3323 bonds, 3 pseudobonds, 419 residues, 2 models selected
> color sel forest green
> select clear
> select ::name="GTP"
450 atoms, 474 bonds, 12 residues, 6 models selected
> color sel yellow
> select clear
> save /Users/shroh/Dropbox/TBC/0_Model_pool/ChimeraX/interface1.cxs
> includeMaps true
> show #!1 atoms
> hide #!1 atoms
> select clear
> select ::name="GTP"
450 atoms, 474 bonds, 12 residues, 6 models selected
> show sel & #!1 atoms
> style sel & #!1 sphere
Changed 64 atom styles
> show #!2 models
> hide #!1 models
> show #!1 models
> show #!3 models
> show #4 models
> show #5 models
> show #6 models
> show #7 models
> select ::name="GTP"
450 atoms, 474 bonds, 12 residues, 6 models selected
> style sel sphere
Changed 450 atom styles
> show sel atoms
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #4 models
> hide #5 models
> hide #6 models
> hide #7 models
> show #!1 models
> select clear
[Repeated 1 time(s)]
> open /Users/shroh/Dropbox/TBC/0_Model_pool/Z_7pjf3.pdb
Summary of feedback from opening
/Users/shroh/Dropbox/TBC/0_Model_pool/Z_7pjf3.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 10 GLY A 29 1 20
Start residue of secondary structure not found: HELIX 2 2 ASP A 47 THR A 51 1
5
Start residue of secondary structure not found: HELIX 3 3 PRO A 72 THR A 80 1
9
Start residue of secondary structure not found: HELIX 4 4 HIS A 88 GLU A 90 1
3
Start residue of secondary structure not found: HELIX 5 5 ASN A 102 TYR A 108
1 7
53 messages similar to the above omitted
Chain information for Z_7pjf3.pdb #8
---
Chain | Description
a | No description available
b | No description available
30 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Computing secondary structure
> close #1
> close #8
> open /Users/shroh/Dropbox/TBC/0_Model_pool/Z_7pjf3.pdb
Summary of feedback from opening
/Users/shroh/Dropbox/TBC/0_Model_pool/Z_7pjf3.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 10 GLY A 29 1 20
Start residue of secondary structure not found: HELIX 2 2 ASP A 47 THR A 51 1
5
Start residue of secondary structure not found: HELIX 3 3 PRO A 72 THR A 80 1
9
Start residue of secondary structure not found: HELIX 4 4 HIS A 88 GLU A 90 1
3
Start residue of secondary structure not found: HELIX 5 5 ASN A 102 TYR A 108
1 7
53 messages similar to the above omitted
Chain information for Z_7pjf3.pdb #1
---
Chain | Description
a | No description available
b | No description available
30 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Computing secondary structure
> matchmaker #!1 to #7/b pairing bs
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bs
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 6_DEG(e)C(NC)_abTub_GTP_241114.pdb, chain b (#7) with Z_7pjf3.pdb,
chain b (#1), sequence alignment score = 1952.8
RMSD between 418 pruned atom pairs is 0.764 angstroms; (across all 428 pairs:
0.971)
Drag select of 13 residues
> select up
307 atoms, 309 bonds, 38 residues, 1 model selected
> select up
2917 atoms, 2982 bonds, 374 residues, 1 model selected
> select up
2922 atoms, 2986 bonds, 375 residues, 1 model selected
> select up
3342 atoms, 3415 bonds, 428 residues, 1 model selected
> color sel indigo
Drag select of 20 residues
> select up
313 atoms, 319 bonds, 40 residues, 1 model selected
> select up
1165 atoms, 1190 bonds, 150 residues, 1 model selected
> select up
1203 atoms, 1228 bonds, 156 residues, 1 model selected
> select up
2983 atoms, 3049 bonds, 383 residues, 1 model selected
> color sel forest green
> select clear
Drag select of 25 residues, 1 pseudobonds
> select up
381 atoms, 384 bonds, 1 pseudobond, 52 residues, 2 models selected
> color sel forest green
> select clear
Drag select of 81 residues, 1 pseudobonds
> select up
1176 atoms, 1191 bonds, 1 pseudobond, 158 residues, 2 models selected
> select up
3251 atoms, 3323 bonds, 1 pseudobond, 419 residues, 2 models selected
> select up
3284 atoms, 3358 bonds, 1 pseudobond, 421 residues, 2 models selected
> select up
6659 atoms, 6807 bonds, 4 pseudobonds, 851 residues, 2 models selected
> select down
3284 atoms, 3358 bonds, 1 pseudobond, 421 residues, 2 models selected
> color sel forest green
> select ::name="GTP"
450 atoms, 475 bonds, 12 residues, 6 models selected
> color sel yellow
> show #!2 models
> show #!3 models
> show #4 models
> show #5 models
> show #6 models
> show #7 models
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #5 models
> hide #4 models
> hide #6 models
> hide #7 models
> show #!1 models
> select clear
> show all
> hide #!1 atoms
> show #1,2,3,4,5,6,7
> show cartoons #1,2,3,4,5,6,7
Expected ',' or a keyword
> show #1,2,3,4,5,6,7 cartoons
> show #!2 models
> show #!3 models
> show #4 models
> show #5 models
> show #6 models
> show #7 models
> hide atoms
> show cartoons
> select ::name="GTP"
450 atoms, 475 bonds, 12 residues, 6 models selected
> show sel surfaces
> select clear
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #7 models
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> show #!6 models
> show #7 models
> cartoon style width 1.5 thickness 1
> cartoon style width 1.5 thickness 0.5
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #7 models
> save /Users/shroh/Dropbox/TBC/0_Model_pool/ChimeraX/interface1.cxs
——— End of log from Thu Nov 14 13:28:54 2024 ———
opened ChimeraX session
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> show #!6 models
> show #7 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #7 models
> open
> /Users/shroh/Dropbox/TBC/0_Structure_pool/Map2_TBC_DEG_beta_with_Edensity_cryosparc_P7J211_P22_J1017.mrc
Opened Map2_TBC_DEG_beta_with_Edensity_cryosparc_P7J211_P22_J1017.mrc as #8,
grid size 350,350,350, pixel 0.59, shown at level 0.0718, step 2, values
float32
> open
> /Users/shroh/Dropbox/TBC/0_Structure_pool/Map1_cryosparc_P7_J200_map_sharp_deepEMhancer.mrc
Opened Map1_cryosparc_P7_J200_map_sharp_deepEMhancer.mrc as #9, grid size
350,350,350, pixel 0.59, shown at level 0.0378, step 2, values float32
> open
> /Users/shroh/Dropbox/TBC/0_Structure_pool/Map3_cryosparc_P22_J1999_map_sharp_deepEM.mrc
Opened Map3_cryosparc_P22_J1999_map_sharp_deepEM.mrc as #10, grid size
300,300,300, pixel 0.76, shown at level 0.0241, step 2, values float32
> open
> /Users/shroh/Dropbox/TBC/0_Structure_pool/Map4_cryosparc_P22_J2169_map_sharp_patched_deepEM.mrc
Opened Map4_cryosparc_P22_J2169_map_sharp_patched_deepEM.mrc as #11, grid size
320,320,320, pixel 1.02, shown at level 0.00198, step 2, values float32
> open
> "/Users/shroh/Dropbox/TBC/0_Structure_pool/Map5_cryosparc_P22_J2345_map_sharp
> (1).mrc"
Opened Map5_cryosparc_P22_J2345_map_sharp (1).mrc as #12, grid size
256,256,256, pixel 1.08, shown at level 0.0158, step 1, values float32
> open
> "/Users/shroh/Dropbox/TBC/0_Structure_pool/Map6_cryosparc_P22_J2347_map_sharp
> (2).mrc"
Opened Map6_cryosparc_P22_J2347_map_sharp (2).mrc as #13, grid size
256,256,256, pixel 1.08, shown at level 0.0123, step 1, values float32
> volume #8 step 1
> volume #8 level 0.2068
> volume #9 level 0.1681
> volume #10 level 0.09914
> volume #11 level 0.08765
> volume #12 level 0.1034
> volume #13 level 0.1223
> volume #8 level 0.2718
> volume #9 level 0.2488
> volume #10 level 0.1611
> volume #11 level 0.1699
> volume #12 level 0.213
> volume #13 level 0.3136
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> hide #!12 models
> hide #!13 models
> select clear
> open /Users/shroh/Dropbox/TBC/0_Model_pool/tubulin_reference/Z_7pjf3.pdb
> format pdb
No such file/path:
/Users/shroh/Dropbox/TBC/0_Model_pool/tubulin_reference/Z_7pjf3.pdb
> open /Users/shroh/Dropbox/TBC/0_Structure_pool/tubulin_reference/Z_7pjf3.pdb
Summary of feedback from opening
/Users/shroh/Dropbox/TBC/0_Structure_pool/tubulin_reference/Z_7pjf3.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 10 GLY A 29 1 20
Start residue of secondary structure not found: HELIX 2 2 ASP A 47 THR A 51 1
5
Start residue of secondary structure not found: HELIX 3 3 PRO A 72 THR A 80 1
9
Start residue of secondary structure not found: HELIX 4 4 HIS A 88 GLU A 90 1
3
Start residue of secondary structure not found: HELIX 5 5 ASN A 102 TYR A 108
1 7
53 messages similar to the above omitted
Chain information for Z_7pjf3.pdb #14
---
Chain | Description
a | No description available
b | No description available
30 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #!14 to #1/a pairing bs
Computing secondary structure
Parameters
---
Chain pairing | bs
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 Z_7pjf3.pdb, chain a (#1) with Z_7pjf3.pdb, chain a (#14), sequence
alignment score = 2216.5
RMSD between 419 pruned atom pairs is 0.000 angstroms; (across all 419 pairs:
0.000)
> hide #!1 models
> matchmaker #!14 to #7/b pairing bs
Computing secondary structure
Parameters
---
Chain pairing | bs
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 6_DEG(e)C(NC)_abTub_GTP_241114.pdb, chain b (#7) with Z_7pjf3.pdb,
chain b (#14), sequence alignment score = 1952.8
RMSD between 418 pruned atom pairs is 0.764 angstroms; (across all 428 pairs:
0.971)
> show #!1 models
> hide #!1 models
Drag select of 9 atoms, 263 residues, 3 pseudobonds, 7 bonds
> select up
2477 atoms, 2525 bonds, 3 pseudobonds, 319 residues, 2 models selected
> select up
3251 atoms, 3323 bonds, 3 pseudobonds, 419 residues, 2 models selected
> select up
3284 atoms, 3358 bonds, 3 pseudobonds, 421 residues, 2 models selected
> delete atoms (#!14 & sel)
> delete bonds (#!14 & sel)
> molmap #14 6
Opened Z_7pjf3.pdb map 6 as #15, grid size 46,44,49, pixel 2, shown at level
0.105, step 1, values float32
> volume #15 level 0.3943
> show #!6 models
> hide #!6 models
> show #7 models
> select #8
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #8,1,0,0,13.882,0,1,0,44.252,0,0,1,10.156
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.95787,0.23538,-0.16457,16.282,-0.02694,0.6441,0.76446,-14.227,0.28594,-0.72782,0.62331,96.935
> view matrix models
> #8,0.87037,0.48974,-0.051111,-12.899,-0.34273,0.67708,0.65123,23.514,0.35354,-0.54929,0.75716,58.858
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.87037,0.48974,-0.051111,-11.522,-0.34273,0.67708,0.65123,44.648,0.35354,-0.54929,0.75716,68.015
> ui tool show "Fit in Map"
> fitmap #8 inMap #13
Fit map Map2_TBC_DEG_beta_with_Edensity_cryosparc_P7J211_P22_J1017.mrc in map
Map6_cryosparc_P22_J2347_map_sharp (2).mrc using 204748 points
correlation = 0.4142, correlation about mean = 0.0567, overlap = 9912
steps = 108, shift = 4.47, angle = 5.17 degrees
Position of Map2_TBC_DEG_beta_with_Edensity_cryosparc_P7J211_P22_J1017.mrc
(#8) relative to Map6_cryosparc_P22_J2347_map_sharp (2).mrc (#13) coordinates:
Matrix rotation and translation
0.83984561 0.54233911 -0.02297071 -12.15947092
-0.41946677 0.67526615 0.60668218 57.56245858
0.34453881 -0.49988392 0.79461254 60.82544903
Axis -0.73209957 -0.24314278 -0.63632681
Axis point 0.00000000 80.08452564 -34.46110087
Rotation angle (degrees) 49.09080224
Shift along axis -43.79881661
> ui tool show "Map Filter"
> volume gaussian #13 sDev 2.83
Opened Map6_cryosparc_P22_J2347_map_sharp (2).mrc gaussian as #16, grid size
256,256,256, pixel 1.08, shown at step 1, values float32
> fitmap #8 inMap #16
Fit map Map2_TBC_DEG_beta_with_Edensity_cryosparc_P7J211_P22_J1017.mrc in map
Map6_cryosparc_P22_J2347_map_sharp (2).mrc gaussian using 204748 points
correlation = 0.8326, correlation about mean = 0.2049, overlap = 1.245e+04
steps = 400, shift = 19.7, angle = 39.5 degrees
Position of Map2_TBC_DEG_beta_with_Edensity_cryosparc_P7J211_P22_J1017.mrc
(#8) relative to Map6_cryosparc_P22_J2347_map_sharp (2).mrc gaussian (#16)
coordinates:
Matrix rotation and translation
0.99749412 -0.06665117 0.02373005 42.96810428
0.05242639 0.92156351 0.38467153 4.99535607
-0.04750756 -0.38246351 0.92274845 82.81070540
Axis -0.98403191 0.09137907 0.15274510
Axis point 0.00000000 223.00965927 25.55585888
Rotation angle (degrees) 22.94154193
Shift along axis -29.17658544
> view matrix models
> #8,0.99749,-0.066651,0.02373,42.181,0.052426,0.92156,0.38467,3.2151,-0.047508,-0.38246,0.92275,82.589
> fitmap #8 inMap #16
Fit map Map2_TBC_DEG_beta_with_Edensity_cryosparc_P7J211_P22_J1017.mrc in map
Map6_cryosparc_P22_J2347_map_sharp (2).mrc gaussian using 204748 points
correlation = 0.8326, correlation about mean = 0.2048, overlap = 1.245e+04
steps = 52, shift = 1.95, angle = 0.00533 degrees
Position of Map2_TBC_DEG_beta_with_Edensity_cryosparc_P7J211_P22_J1017.mrc
(#8) relative to Map6_cryosparc_P22_J2347_map_sharp (2).mrc gaussian (#16)
coordinates:
Matrix rotation and translation
0.99749057 -0.06669505 0.02375608 42.98125521
0.05245322 0.92153173 0.38474399 4.97232938
-0.04755250 -0.38253242 0.92271757 82.83387882
Axis -0.98401583 0.09145175 0.15280515
Axis point 0.00000000 223.02084806 25.62478133
Rotation angle (degrees) 22.94640731
Shift along axis -29.18206398
> hide #!8 models
> show #!9 models
> select #9
2 models selected
> view matrix models #9,1,0,0,21.883,0,1,0,43.316,0,0,1,33.188
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.94513,-0.014905,-0.32636,63.144,0.31913,0.2559,0.91251,-14.771,0.069915,-0.96659,0.24662,196.39
> view matrix models
> #9,0.7536,0.46759,0.462,-43.113,-0.63556,0.69771,0.33055,110.26,-0.16778,-0.54273,0.82298,122.86
> view matrix models
> #9,0.85731,0.43901,0.26887,-32.162,-0.50471,0.81966,0.27096,89.83,-0.10143,-0.368,0.92428,88.031
> view matrix models
> #9,0.64289,0.73863,0.20277,-30.116,-0.74046,0.53159,0.41126,129.85,0.19598,-0.41454,0.88868,62.618
> fitmap #9 inMap #16
Fit map Map1_cryosparc_P7_J200_map_sharp_deepEMhancer.mrc in map
Map6_cryosparc_P22_J2347_map_sharp (2).mrc gaussian using 23532 points
correlation = 0.8615, correlation about mean = 0.1835, overlap = 1565
steps = 272, shift = 9.87, angle = 51.6 degrees
Position of Map1_cryosparc_P7_J200_map_sharp_deepEMhancer.mrc (#9) relative to
Map6_cryosparc_P22_J2347_map_sharp (2).mrc gaussian (#16) coordinates:
Matrix rotation and translation
0.99904450 -0.02449104 0.03619778 37.07147995
0.00914387 0.92703763 0.37485680 10.10667704
-0.04273734 -0.37416764 0.92637579 80.12600480
Axis -0.99350276 0.10469920 0.04461320
Axis point 0.00000000 216.75681334 6.23526589
Rotation angle (degrees) 22.14559290
Shift along axis -32.19777891
> hide #!9 models
> show #!10 models
> select #10
2 models selected
> view matrix models
> #10,0.89375,0.44826,-0.016511,-33.233,-0.39205,0.79849,0.45685,24.139,0.21797,-0.40184,0.88939,27.224
> view matrix models
> #10,0.89564,0.38307,-0.22601,-5.2707,-0.30113,0.89623,0.32572,15.614,0.32733,-0.22367,0.91805,-8.3958
> view matrix models
> #10,0.92562,0.31568,-0.20875,-3.5108,-0.2388,0.91508,0.32496,5.9187,0.29361,-0.25094,0.9224,-1.7158
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.92562,0.31568,-0.20875,14.377,-0.2388,0.91508,0.32496,30.303,0.29361,-0.25094,0.9224,11.947
> fitmap #10 inMap #16
Fit map Map3_cryosparc_P22_J1999_map_sharp_deepEM.mrc in map
Map6_cryosparc_P22_J2347_map_sharp (2).mrc gaussian using 17294 points
correlation = 0.8545, correlation about mean = 0.2309, overlap = 1011
steps = 188, shift = 14.5, angle = 25.3 degrees
Position of Map3_cryosparc_P22_J1999_map_sharp_deepEM.mrc (#10) relative to
Map6_cryosparc_P22_J2347_map_sharp (2).mrc gaussian (#16) coordinates:
Matrix rotation and translation
0.99811610 -0.02377700 0.05655894 23.91413889
0.00287096 0.93894308 0.34406053 -1.56406851
-0.06128635 -0.34324997 0.93724247 72.01338179
Axis -0.98489847 0.16886930 0.03818585
Axis point 0.00000000 206.50164058 30.85158894
Rotation angle (degrees) 20.42154950
Shift along axis -21.06722947
> hide #!10 models
> show #!11 models
> select #11
2 models selected
> view matrix models #11,1,0,0,-16.358,0,1,0,-35.669,0,0,1,-28.827
> fitmap #11 inMap #16
Fit map Map4_cryosparc_P22_J2169_map_sharp_patched_deepEM.mrc in map
Map6_cryosparc_P22_J2347_map_sharp (2).mrc gaussian using 9567 points
correlation = 0.7953, correlation about mean = 0.1643, overlap = 499.9
steps = 112, shift = 14.6, angle = 0.479 degrees
Position of Map4_cryosparc_P22_J2169_map_sharp_patched_deepEM.mrc (#11)
relative to Map6_cryosparc_P22_J2347_map_sharp (2).mrc gaussian (#16)
coordinates:
Matrix rotation and translation
0.99997707 -0.00377248 -0.00562448 -23.25037805
0.00374480 0.99998086 -0.00492427 -24.54967044
0.00564295 0.00490309 0.99997206 -25.60697505
Axis 0.58725339 -0.67330812 0.44921002
Axis point 3835.00404502 0.00000000 -3248.64188525
Rotation angle (degrees) 0.47941195
Shift along axis -8.62728047
> hide #!11 models
> show #!12 models
> show #!8 models
> show #!9 models
> show #!10 models
> show #!11 models
> show #!13 models
> fitmap #9 inMap #15
Fit map Map1_cryosparc_P7_J200_map_sharp_deepEMhancer.mrc in map Z_7pjf3.pdb
map 6 using 23532 points
correlation = 0.5009, correlation about mean = 0.1297, overlap = 1551
steps = 128, shift = 3.32, angle = 10.6 degrees
Position of Map1_cryosparc_P7_J200_map_sharp_deepEMhancer.mrc (#9) relative to
Z_7pjf3.pdb map 6 (#15) coordinates:
Matrix rotation and translation
-0.89392411 0.37333539 -0.24803299 233.80132702
0.07501336 0.67018238 0.73839595 -131.07580977
0.44189668 0.64146416 -0.62709733 2.11676035
Axis -0.12789719 -0.91033153 -0.39362267
Axis point 122.11023285 0.00000000 55.89499791
Rotation angle (degrees) 157.73170228
Shift along axis 88.58670504
> fitmap #8 inMap #15
Fit map Map2_TBC_DEG_beta_with_Edensity_cryosparc_P7J211_P22_J1017.mrc in map
Z_7pjf3.pdb map 6 using 204748 points
correlation = 0.478, correlation about mean = 0.144, overlap = 1.211e+04
steps = 120, shift = 2.48, angle = 10.4 degrees
Position of Map2_TBC_DEG_beta_with_Edensity_cryosparc_P7J211_P22_J1017.mrc
(#8) relative to Z_7pjf3.pdb map 6 (#15) coordinates:
Matrix rotation and translation
-0.87545296 0.41400060 -0.24937045 227.07860441
0.10744732 0.66977903 0.73474563 -133.92544491
0.47120823 0.61644105 -0.63084329 1.21289725
Axis -0.14938155 -0.90986470 -0.38708058
Axis point 120.55515402 0.00000000 56.33575039
Rotation angle (degrees) 156.67281563
Shift along axis 87.46319184
> fitmap #10 inMap #15
Fit map Map3_cryosparc_P22_J1999_map_sharp_deepEM.mrc in map Z_7pjf3.pdb map 6
using 17294 points
correlation = 0.4436, correlation about mean = 0.09829, overlap = 787.4
steps = 72, shift = 1.07, angle = 4.46 degrees
Position of Map3_cryosparc_P22_J1999_map_sharp_deepEM.mrc (#10) relative to
Z_7pjf3.pdb map 6 (#15) coordinates:
Matrix rotation and translation
-0.88393685 0.30802601 -0.35181761 258.89783407
-0.04547377 0.69218873 0.72028251 -135.29866380
0.46538993 0.65268273 -0.59784402 -8.94594070
Axis -0.07570387 -0.91517710 -0.39587851
Axis point 130.70449621 0.00000000 59.16981658
Rotation angle (degrees) 153.48224714
Shift along axis 107.76417555
> fitmap #11 inMap #15
Fit map Map4_cryosparc_P22_J2169_map_sharp_patched_deepEM.mrc in map
Z_7pjf3.pdb map 6 using 9567 points
correlation = 0.3986, correlation about mean = 0.1095, overlap = 357.7
steps = 108, shift = 1.46, angle = 2.61 degrees
Position of Map4_cryosparc_P22_J2169_map_sharp_patched_deepEM.mrc (#11)
relative to Z_7pjf3.pdb map 6 (#15) coordinates:
Matrix rotation and translation
-0.91386602 0.12906839 -0.38495487 343.25795675
-0.05523842 0.89978820 0.43281625 -190.81318702
0.40224075 0.41680036 -0.81515633 40.23344722
Axis -0.01980590 -0.97347810 -0.22792129
Axis point 165.00886811 0.00000000 80.05045804
Rotation angle (degrees) 156.15140448
Shift along axis 169.78386703
> fitmap #12 inMap #15
Fit map Map5_cryosparc_P22_J2345_map_sharp (1).mrc in map Z_7pjf3.pdb map 6
using 56998 points
correlation = 0.4152, correlation about mean = 0.1359, overlap = 2388
steps = 68, shift = 1.2, angle = 2.13 degrees
Position of Map5_cryosparc_P22_J2345_map_sharp (1).mrc (#12) relative to
Z_7pjf3.pdb map 6 (#15) coordinates:
Matrix rotation and translation
-0.90850832 0.12392018 -0.39906945 316.34937962
-0.06908159 0.89733425 0.43591165 -157.87590756
0.41211694 0.42359772 -0.80667503 36.97409928
Axis -0.01476631 -0.97273738 -0.23143884
Axis point 151.57496541 0.00000000 73.01899143
Rotation angle (degrees) 155.35715208
Shift along axis 140.34324253
> fitmap #13 inMap #15
Fit map Map6_cryosparc_P22_J2347_map_sharp (2).mrc in map Z_7pjf3.pdb map 6
using 43958 points
correlation = 0.4706, correlation about mean = 0.1625, overlap = 2803
steps = 48, shift = 0.144, angle = 0.265 degrees
Position of Map6_cryosparc_P22_J2347_map_sharp (2).mrc (#13) relative to
Z_7pjf3.pdb map 6 (#15) coordinates:
Matrix rotation and translation
-0.90358988 0.11657596 -0.41223218 317.57861895
-0.09252564 0.88644528 0.45349065 -155.45810223
0.41828738 0.44791161 -0.79019672 31.02826849
Axis -0.00651410 -0.96971625 -0.24414743
Axis point 151.71676090 0.00000000 72.02568863
Rotation angle (degrees) 154.64483431
Shift along axis 141.10603658
> select clear
> save /Users/shroh/Dropbox/TBC/0_Structure_pool/ChimeraX/overall.cxs
> includeMaps true
> hide #7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> hide #!13 models
> hide #!14 models
> hide #!15 models
> close #15-16
> show #!14 models
> hide #!14 models
> close #14
> show #!2 models
> show #!9 models
> hide #!9 models
> select clear
> show #!9 models
> color zone #9 near #2 distance 3
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!9 models
> show #!3 models
> show #!8 models
> color zone #8 near #3 distance 3
> hide #!3 models
> color zone #8 near #3 distance 4
> color zone #8 near #3 distance 5
> show #!3 models
> color zone #8 near #3 distance 5
> hide #!3 models
> hide #!8 models
> show #!4 models
> show #!11 models
> hide #!11 models
> hide #!4 models
> show #!5 models
> show #!11 models
> show #!10 models
> hide #!11 models
> hide #!5 models
> show #!4 models
> color zone #10 near #3 distance 5
> hide #!10 models
> show #!10 models
> hide #!10 models
> select clear
> show #!10 models
> color zone #10 near #3 distance 10
> color zone #10 near #3 distance 3
> hide #!10 models
> select clear
[Repeated 1 time(s)]Drag select of DEG(e)C_bTub_GTP_241017.pdb_H SES surface,
DEG(e)C_bTub_GTP_241017.pdb_I SES surface, 1968 residues
> color zone #10 near #4 distance 10
> show #!10 models
> select clear
> hide #!10 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!11 models
> color zone #11 near #5 distance 10
> color zone #12 near #6 distance 10
> hide #!11 models
> hide #!4 models
> show #!5 models
> show #!11 models
> hide #!11 models
Drag select of 6 residues
> select up
217 atoms, 219 bonds, 14 residues, 1 model selected
> select up
2955 atoms, 2978 bonds, 184 residues, 1 model selected
> color sel orange
> select clear
> color zone #11 near #5 distance 10
> show #!11 models
> show #!12 models
> hide #!5 models
> show #!13 models
> hide #!12 models
> hide #!11 models
> color zone #13 near #7 distance 10
> show #!12 models
> show #!11 models
> show #!10 models
> show #!9 models
> show #!8 models
> show #7 models
> hide #7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> hide #!12 models
> hide #!13 models
> show #7 models
> show #!6 models
> hide #!6 models
> hide #7 models
> show #!2 models
> show #!13 models
> hide #!13 models
> hide #!2 models
> show #!8 models
> hide #!8 models
> show #!9 models
> show #!2 models
> hide #!2 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!9 models
> show #!8 models
> hide #!13 models
> show #7 models
> hide #!8 models
> hide #7 models
> show #7 models
> show #!6 models
> hide #7 models
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> show #7 models
> select ::name="GTP"
450 atoms, 475 bonds, 12 residues, 6 models selected
> show (#!2-6 & sel) target ab
> show sel & #!2-6 surfaces
> select clear
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #7 models
> cartoon style width 1.5 thickness 0.3
> show #!2 models
> show #!8 models
> hide #!8 models
> show #!8 models
> show #!9 models
> hide #!9 models
> show #!10 models
> hide #!10 models
> select clear
> lighting full
> graphics silhouettes true color black width 2
> hide #!2 models
> hide #!8 models
> show #!9 models
> save /Users/shroh/Desktop/tbc/overall_1.tif pixelSize 0.1
> transparentBackground true
> hide #!9 models
> show #!8 models
> save /Users/shroh/Desktop/tbc/overall_2.tif pixelSize 0.1
> transparentBackground true
> hide #!8 models
> show #!10 models
> save /Users/shroh/Desktop/tbc/overall_3.tif pixelSize 0.1
> transparentBackground true
> hide #!10 models
> show #!11 models
> save /Users/shroh/Desktop/tbc/overall_4.tif pixelSize 0.1
> transparentBackground true
> hide #!11 models
> show #!12 models
> save /Users/shroh/Desktop/tbc/overall_5.tif pixelSize 0.1
> transparentBackground true
> hide #!12 models
> show #!13 models
> save /Users/shroh/Desktop/tbc/overall_6.tif pixelSize 0.1
> transparentBackground true
> hide #!13 models
> show #!2 models
> lighting shadows false
> save /Users/shroh/Desktop/tbc/overall_M1.tif pixelSize 0.1
> transparentBackground true
> hide #!2 models
> show #!3 models
> save /Users/shroh/Desktop/tbc/overall_M2.tif pixelSize 0.1
> transparentBackground true
> hide #!3 models
> show #!4 models
> save /Users/shroh/Desktop/tbc/overall_M3.tif pixelSize 0.1
> transparentBackground true
> hide #!4 models
> show #!5 models
> save /Users/shroh/Desktop/tbc/overall_M4.tif pixelSize 0.1
> transparentBackground true
> hide #!5 models
> show #!6 models
> save /Users/shroh/Desktop/tbc/overall_M5.tif pixelSize 0.1
> transparentBackground true
> hide #!6 models
> show #7 models
> select ::name="GTP"
450 atoms, 475 bonds, 12 residues, 6 models selected
> show #7 atoms
> hide #7 atoms
> hide #7 models
> show #!6 models
> select clear
> hide #!6 cartoons
> show #7 models
> save /Users/shroh/Desktop/tbc/overall_M6.tif pixelSize 0.1
> transparentBackground true
> save /Users/shroh/Dropbox/TBC/0_Structure_pool/ChimeraX/overall1.cxs
> view name overall1
> save /Users/shroh/Dropbox/TBC/0_Structure_pool/ChimeraX/overall1.cxs
> save /Users/shroh/Dropbox/TBC/0_Structure_pool/ChimeraX/overall1.cxs
> includeMaps true
——— End of log from Thu Nov 14 19:18:36 2024 ———
opened ChimeraX session
> hide #7 models
> hide #!6 models
> show #!3 models
> save /Users/airen/Dropbox/0.SNU_cryoEMlab/project/TBC/figure/model1-new.png
> transparentBackground true width 1200
OpenGL version: 4.1 INTEL-20.6.1
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,2
Processor Name: Quad-Core Intel Core i5
Processor Speed: 2 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 512 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 1968.120.12.0.0 (iBridge: 20.16.5058.0.0,0)
OS Loader Version: 577~170
Software:
System Software Overview:
System Version: macOS 13.4 (22F66)
Kernel Version: Darwin 22.5.0
Time since boot: 5 days, 2 hours, 26 minutes
Graphics/Displays:
Intel Iris Plus Graphics:
Chipset Model: Intel Iris Plus Graphics
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x8a53
Revision ID: 0x0007
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-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: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
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: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
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: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
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
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
File attachment: model1-full.png
Attachments (1)
Change History (3)
by , 10 months ago
| Attachment: | model1-full.png added |
|---|
comment:1 by , 10 months ago
| Component: | Unassigned → Input/Output |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Silhouette outlines incorrect in saved image |
comment:2 by , 10 months ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
Unfortunately this is a bug in Apple's Intel graphics driver on a specific model MacBook Pro (MacBookPro16,2). It effects rendering of silhouette edges. You can turn off silhouette edges (command "graphics silhouettes false" or use the Graphics toolbar Silhouettes button) and it will render correctly. If you need the silhouette edges then you can save a session and copy it to another computer to save the image. Apple has not made computers with Intel graphics for years now and will not fix this. This bug has been present in all ChimeraX versions since this MacBook Pro was released in 2020.
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