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Opened 5 years ago
Closed 5 years ago
#3582 closed defect (worksforme)
--offscreen does not work on Linux (or Mac, or Windows)
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: Darwin-19.5.0-x86_64-i386-64bit
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
Re: [chimerax-users] OpenGL error with nogui?
This is a follow up of my mail to Greg Couch regarding a --nogui error we are getting, we can run a script using a python interface, but only without the --nogui flag. I atached the script I wrote.
See at the end for the new error with the --offscreen flag.
Thanks!
Next time, please use the Help / Report a Bug dialog to report an issue. It captures details about your setup that would help diagnose this.
That said, ChimeraX --offscreen is what you need if you want to make images without the GUI and it only works on Linux at this time. The only issue with offscreen rendering that I'm aware of in the 1.0 release is that it doesn't work for labels. That has been fixed in the daily builds.
-- Greg
On 8/1/2020 1:41 AM, Fabian Glaser wrote:
Dear gurus,
I am trying to produce a series of figures on the fly with chimeraX, using a python script of the following format (this is only a simple demo):
test.py:
#!/usr/bin/env python3
import sys
from chimerax.core.commands import run
run(session, "open 1d66")
run(session, "color red")
run (session, "save fig1.png”)
==
This works like a charm with the gui, but without the gui it gives the following error, stops and no figure is produced, we tried both in Mac and linux. We are interest in the —nogui option:
.../MacOS/ChimeraX --script "test.py 1d66" —nogui
Executing: surface sel-residues enclose sel-residues
Executing: transparency 0 ribbons
Set transparency of 542 residues
Executing: ~select
Nothing selected
Nothing selected
Executing: save fig1.jpg
Unable to save images because OpenGL rendering is not available
======
I also tried with the --offscreen flag on linux
/home/avivr/chimerax/chimerax_1.0/usr/bin/chimerax --script "test.py inp1.txt" --offscreen --nogui
Traceback (most recent call last):
File "/home/avivr/chimerax/chimerax_1.0/usr/lib/ucsf-chimerax/lib/python3.7/runpy.py", line 193, in _run_module_as_main
"__main__", mod_spec)
File "/home/avivr/chimerax/chimerax_1.0/usr/lib/ucsf-chimerax/lib/python3.7/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/home/avivr/chimerax/chimerax_1.0/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/ChimeraX_main.py", line 895, in <module>
exit_code = init(sys.argv)
File "/home/avivr/chimerax/chimerax_1.0/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/ChimeraX_main.py", line 453, in init
sess = session.Session(app_name, debug=opts.debug, silent=opts.silent)
File "/home/avivr/chimerax/chimerax_1.0/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/core/session.py", line 441, in __init__
self.logger = logger.Logger(self)
File "/home/avivr/chimerax/chimerax_1.0/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/core/session.py", line 501, in __setattr__
if not name.startswith('_') and self.snapshot_methods(value, base_type=StateManager) is not None:
File "/home/avivr/chimerax/chimerax_1.0/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/core/session.py", line 535, in snapshot_methods
from chimerax import graphics as gr
File "/home/avivr/chimerax/chimerax_1.0/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/graphics/__init__.py", line 34, in <module>
from .opengl import Texture, Lighting, Material
File "/home/avivr/chimerax/chimerax_1.0/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/graphics/opengl.py", line 61, in <module>
from OpenGL import GL
File "/home/avivr/chimerax/chimerax_1.0/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/PyOpenGL-3.1.5-py3.7.egg/OpenGL/GL/__init__.py", line 4, in <module>
from OpenGL.GL.VERSION.GL_1_1 import *
File "/home/avivr/chimerax/chimerax_1.0/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/PyOpenGL-3.1.5-py3.7.egg/OpenGL/GL/VERSION/GL_1_1.py", line 14, in <module>
from OpenGL.raw.GL.VERSION.GL_1_1 import *
File "/home/avivr/chimerax/chimerax_1.0/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/PyOpenGL-3.1.5-py3.7.egg/OpenGL/raw/GL/VERSION/GL_1_1.py", line 7, in <module>
from OpenGL.raw.GL import _errors
File "/home/avivr/chimerax/chimerax_1.0/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/PyOpenGL-3.1.5-py3.7.egg/OpenGL/raw/GL/_errors.py", line 4, in <module>
_error_checker = _ErrorChecker( _p, _p.GL.glGetError )
AttributeError: 'NoneType' object has no attribute 'glGetError'
Any suggestion?
Thanks!
Fabian
Log:
UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/andrewL/chimerax/NIPS_IQ-M1.cxs"
Log from Tue Jul 21 08:59:41 2020UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/andrewL/chimerax/NIPS_IQ-M1.cxs"
Log from Tue Jul 21 07:57:59 2020UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/andrewL/chimerax/NIPS_IQ-M1.cxs"
Log from Tue Jul 21 07:53:47 2020UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/andrewL/chimerax/NIPS_IQ-M1.f2.cxs"
Log from Sun Jul 19 14:23:32 2020UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/andrewL/chimerax/NIPS_IQ-M1.cxs"
Log from Sun Jul 19 11:52:36 2020UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/ayalaS/amber/ARD1_YEAST.6HD5/full/md.12.OPC3/3-INPUT/6HD5.U.SCP.FH.pdb"
Summary of feedback from opening /Users/admin/Dropbox (Technion
Dropbox)/PROJECTS/ayalaS/amber/ARD1_YEAST.6HD5/full/md.12.OPC3/3-INPUT/6HD5.U.SCP.FH.pdb
---
warnings | Duplicate atom serial number found: 0
Duplicate atom serial number found: 0
Duplicate atom serial number found: 0
Duplicate atom serial number found: 0
Duplicate atom serial number found: 0
1858 messages similar to the above omitted
Chain information for 6HD5.U.SCP.FH.pdb #1
---
Chain | Description
u | No description available
> show
> help runscript
> close
> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/alexB/chimerax/test.cxc"
> open 1WMB
1wmb title:
Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more
info...]
Chain information for 1wmb #1
---
Chain | Description
A B | D(-)-3-hydroxybutyrate dehydrogenase
Non-standard residues in 1wmb #1
---
CAC — cacodylate ion (dimethylarsinate)
MG — magnesium ion
1wmb mmCIF Assemblies
---
1| author_and_software_defined_assembly
> rainbow chains
> show :138 :< 5
> color byatom
> style stick
Changed 4198 atom styles
> view
executed test.cxc
> set bgColor white
> set bgColor white
> set bgColor white
> set bgColor white
> set bgColor white
> set bgColor white
> help color
> color background black
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color black background
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color black target background
Invalid "target" argument: Character 'k' is not an allowed target, must be one
of acrsbpfl
> color target background black
Invalid "target" argument: Character 'k' is not an allowed target, must be one
of acrsbpfl
> color background black
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/alexB/chimerax/test.cxc"
> open 1WMB
1wmb title:
Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more
info...]
Chain information for 1wmb #2
---
Chain | Description
A B | D(-)-3-hydroxybutyrate dehydrogenase
Non-standard residues in 1wmb #2
---
CAC — cacodylate ion (dimethylarsinate)
MG — magnesium ion
1wmb mmCIF Assemblies
---
1| author_and_software_defined_assembly
> rainbow chains
> ~display
> show :138 :< 5
> color byatom
> color :138 gold
> style stick
Changed 8396 atom styles
> view
executed test.cxc
> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/alexB/chimerax/test.cxc"
> open 1WMB
1wmb title:
Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more
info...]
Chain information for 1wmb #3
---
Chain | Description
A B | D(-)-3-hydroxybutyrate dehydrogenase
Non-standard residues in 1wmb #3
---
CAC — cacodylate ion (dimethylarsinate)
MG — magnesium ion
1wmb mmCIF Assemblies
---
1| author_and_software_defined_assembly
> rainbow chains
> ~display
> show :138 :< 5
> color byatom
> color :138 gold
> style stick
Changed 12594 atom styles
> view :138 :< 10
executed test.cxc
> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/alexB/chimerax/test.cxc"
> open 1WMB
1wmb title:
Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more
info...]
Chain information for 1wmb #4
---
Chain | Description
A B | D(-)-3-hydroxybutyrate dehydrogenase
Non-standard residues in 1wmb #4
---
CAC — cacodylate ion (dimethylarsinate)
MG — magnesium ion
1wmb mmCIF Assemblies
---
1| author_and_software_defined_assembly
> rainbow chains
> ~display
> show :138 :< 5
> color byatom
> color :138 gold
> style stick
Changed 16792 atom styles
> view /a:138 :< 10
executed test.cxc
> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/alexB/chimerax/test.cxc"
> open 1WMB
1wmb title:
Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more
info...]
Chain information for 1wmb #5
---
Chain | Description
A B | D(-)-3-hydroxybutyrate dehydrogenase
Non-standard residues in 1wmb #5
---
CAC — cacodylate ion (dimethylarsinate)
MG — magnesium ion
1wmb mmCIF Assemblies
---
1| author_and_software_defined_assembly
> rainbow chains
> ~display
> show :138 :< 5
> color byatom
> color :138 gold
> style stick
Changed 20990 atom styles
> view /a:138 :< 10
> transparency 80 target r
executed test.cxc
> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/alexB/chimerax/test.cxc"
> open 1WMB
1wmb title:
Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more
info...]
Chain information for 1wmb #6
---
Chain | Description
A B | D(-)-3-hydroxybutyrate dehydrogenase
Non-standard residues in 1wmb #6
---
CAC — cacodylate ion (dimethylarsinate)
MG — magnesium ion
1wmb mmCIF Assemblies
---
1| author_and_software_defined_assembly
> rainbow chains
> ~display
> show :138 :< 5
> color byatom
> color :138 gold
> style stick
Changed 25188 atom styles
> view /a:138 :< 5
> transparency 80 target r
executed test.cxc
> close
> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/alexB/chimerax/test.cxc"
> open 1WMB
1wmb title:
Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more
info...]
Chain information for 1wmb #1
---
Chain | Description
A B | D(-)-3-hydroxybutyrate dehydrogenase
Non-standard residues in 1wmb #1
---
CAC — cacodylate ion (dimethylarsinate)
MG — magnesium ion
1wmb mmCIF Assemblies
---
1| author_and_software_defined_assembly
> rainbow chains
> ~display
> show :138 :< 5
> color byatom
> color :138 gold
> style stick
Changed 4198 atom styles
> view /a:138 :< 5
> transparency 80 target r
executed test.cxc
> close
> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/alexB/chimerax/test.cxc"
> open 1WMB
1wmb title:
Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more
info...]
Chain information for 1wmb #1
---
Chain | Description
A B | D(-)-3-hydroxybutyrate dehydrogenase
Non-standard residues in 1wmb #1
---
CAC — cacodylate ion (dimethylarsinate)
MG — magnesium ion
1wmb mmCIF Assemblies
---
1| author_and_software_defined_assembly
> rainbow chains
> ~display
> show :138 :< 5
> color byatom
> color :138 gold
> style stick
Changed 4198 atom styles
> view /a:138 :< 5
> transparency 80 target r
executed test.cxc
> save "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/alexB/chimerax/test.gif" width 1963 height 1218
> supersample 3
> hbonds
1625 hydrogen bonds found
> ~hbonds
> hbonds :138
4 hydrogen bonds found
> hbonds :138 :< 5
74 hydrogen bonds found
> close
> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/alexB/chimerax/test.cxc"
> open 1WMB 3U09
1wmb title:
Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more
info...]
Chain information for 1wmb #1
---
Chain | Description
A B | D(-)-3-hydroxybutyrate dehydrogenase
Non-standard residues in 1wmb #1
---
CAC — cacodylate ion (dimethylarsinate)
MG — magnesium ion
1wmb mmCIF Assemblies
---
1| author_and_software_defined_assembly
3u09 title:
Crystal structure of 3-ketoacyl-(acyl-carrier-protein) reductase (FabG)(G92D)
from Vibrio cholerae [more info...]
Chain information for 3u09 #2
---
Chain | Description
A B | 3-oxoacyl-[acyl-carrier-protein] reductase FabG
Non-standard residues in 3u09 #2
---
SO4 — sulfate ion
UNX — unknown atom or ion
3u09 mmCIF Assemblies
---
1| author_and_software_defined_assembly
> delete ~/a
> mmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1wmb, chain A (#1) with 3u09, chain A (#2), sequence alignment
score = 570.2
RMSD between 195 pruned atom pairs is 0.869 angstroms; (across all 240 pairs:
2.475)
> rainbow chains
> ~display
> show :138 :< 5
> color byatom
> color :138 gold
> style stick
Changed 4119 atom styles
> view /a:138 :< 5
> hbonds :138
8 hydrogen bonds found
> transparency 80 target r
executed test.cxc
> close
> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/alexB/chimerax/test.cxc"
> open 1WMB 3U09
1wmb title:
Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more
info...]
Chain information for 1wmb #1
---
Chain | Description
A B | D(-)-3-hydroxybutyrate dehydrogenase
Non-standard residues in 1wmb #1
---
CAC — cacodylate ion (dimethylarsinate)
MG — magnesium ion
1wmb mmCIF Assemblies
---
1| author_and_software_defined_assembly
3u09 title:
Crystal structure of 3-ketoacyl-(acyl-carrier-protein) reductase (FabG)(G92D)
from Vibrio cholerae [more info...]
Chain information for 3u09 #2
---
Chain | Description
A B | 3-oxoacyl-[acyl-carrier-protein] reductase FabG
Non-standard residues in 3u09 #2
---
SO4 — sulfate ion
UNX — unknown atom or ion
3u09 mmCIF Assemblies
---
1| author_and_software_defined_assembly
> delete ~/a
> mmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1wmb, chain A (#1) with 3u09, chain A (#2), sequence alignment
score = 570.2
RMSD between 195 pruned atom pairs is 0.869 angstroms; (across all 240 pairs:
2.475)
> rainbow structures
> ~display
> show :138 :< 5
> color byatom
> color :138 gold
> style stick
Changed 4119 atom styles
> view /a:138 :< 5
> hbonds :138
8 hydrogen bonds found
> transparency 80 target r
executed test.cxc
> close #2-3#1
> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/alexB/chimerax/test.cxc"
> open 1WMB 3U09
1wmb title:
Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more
info...]
Chain information for 1wmb #1
---
Chain | Description
A B | D(-)-3-hydroxybutyrate dehydrogenase
Non-standard residues in 1wmb #1
---
CAC — cacodylate ion (dimethylarsinate)
MG — magnesium ion
1wmb mmCIF Assemblies
---
1| author_and_software_defined_assembly
3u09 title:
Crystal structure of 3-ketoacyl-(acyl-carrier-protein) reductase (FabG)(G92D)
from Vibrio cholerae [more info...]
Chain information for 3u09 #2
---
Chain | Description
A B | 3-oxoacyl-[acyl-carrier-protein] reductase FabG
Non-standard residues in 3u09 #2
---
SO4 — sulfate ion
UNX — unknown atom or ion
3u09 mmCIF Assemblies
---
1| author_and_software_defined_assembly
> delete ~/a
> mmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1wmb, chain A (#1) with 3u09, chain A (#2), sequence alignment
score = 570.2
RMSD between 195 pruned atom pairs is 0.869 angstroms; (across all 240 pairs:
2.475)
> rainbow structures
> ~display
> show :138 :< 5
> color byatom
> color :138 gold
> style stick
Changed 4119 atom styles
> view /a:138 :< 5
> hbonds :138
8 hydrogen bonds found
> transparency 80 target r
executed test.cxc
> label
> label
> label
> label :138
> label :138 :< 5
> close
> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/alexB/chimerax/test.cxc"
> open 1WMB 3U09
1wmb title:
Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more
info...]
Chain information for 1wmb #1
---
Chain | Description
A B | D(-)-3-hydroxybutyrate dehydrogenase
Non-standard residues in 1wmb #1
---
CAC — cacodylate ion (dimethylarsinate)
MG — magnesium ion
1wmb mmCIF Assemblies
---
1| author_and_software_defined_assembly
3u09 title:
Crystal structure of 3-ketoacyl-(acyl-carrier-protein) reductase (FabG)(G92D)
from Vibrio cholerae [more info...]
Chain information for 3u09 #2
---
Chain | Description
A B | 3-oxoacyl-[acyl-carrier-protein] reductase FabG
Non-standard residues in 3u09 #2
---
SO4 — sulfate ion
UNX — unknown atom or ion
3u09 mmCIF Assemblies
---
1| author_and_software_defined_assembly
> delete ~/a
> mmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1wmb, chain A (#1) with 3u09, chain A (#2), sequence alignment
score = 570.2
RMSD between 195 pruned atom pairs is 0.869 angstroms; (across all 240 pairs:
2.475)
> rainbow structures
> ~display
> show :138 :< 5
> color byatom
> color :138 gold
> style stick
Changed 4119 atom styles
> view /a:138 :< 4
> hbonds :138
8 hydrogen bonds found
> transparency 90 target r
executed test.cxc
> view :138
> view :138 :< 3
> view :138 :< 2
> view :138 :< 5
> view :138 :< 2
> view :138 :< 1
> view :138 :< 2
> close
> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/alexB/chimerax/test.cxc"
> open 1WMB 3U09
1wmb title:
Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more
info...]
Chain information for 1wmb #1
---
Chain | Description
A B | D(-)-3-hydroxybutyrate dehydrogenase
Non-standard residues in 1wmb #1
---
CAC — cacodylate ion (dimethylarsinate)
MG — magnesium ion
1wmb mmCIF Assemblies
---
1| author_and_software_defined_assembly
3u09 title:
Crystal structure of 3-ketoacyl-(acyl-carrier-protein) reductase (FabG)(G92D)
from Vibrio cholerae [more info...]
Chain information for 3u09 #2
---
Chain | Description
A B | 3-oxoacyl-[acyl-carrier-protein] reductase FabG
Non-standard residues in 3u09 #2
---
SO4 — sulfate ion
UNX — unknown atom or ion
3u09 mmCIF Assemblies
---
1| author_and_software_defined_assembly
> delete ~/a
> mmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1wmb, chain A (#1) with 3u09, chain A (#2), sequence alignment
score = 570.2
RMSD between 195 pruned atom pairs is 0.869 angstroms; (across all 240 pairs:
2.475)
> rainbow structures
> ~display
> show :138 :< 5
> color byatom
> color :138 gold
> style stick
Changed 4119 atom styles
> view /a:138 :< 2
> hbonds :138
8 hydrogen bonds found
> transparency 90 target r
executed test.cxc
> help rainbow
> close
> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/alexB/chimerax/test.cxc"
> open 1WMB 3U09
1wmb title:
Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more
info...]
Chain information for 1wmb #1
---
Chain | Description
A B | D(-)-3-hydroxybutyrate dehydrogenase
Non-standard residues in 1wmb #1
---
CAC — cacodylate ion (dimethylarsinate)
MG — magnesium ion
1wmb mmCIF Assemblies
---
1| author_and_software_defined_assembly
3u09 title:
Crystal structure of 3-ketoacyl-(acyl-carrier-protein) reductase (FabG)(G92D)
from Vibrio cholerae [more info...]
Chain information for 3u09 #2
---
Chain | Description
A B | 3-oxoacyl-[acyl-carrier-protein] reductase FabG
Non-standard residues in 3u09 #2
---
SO4 — sulfate ion
UNX — unknown atom or ion
3u09 mmCIF Assemblies
---
1| author_and_software_defined_assembly
> delete ~/a
> mmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1wmb, chain A (#1) with 3u09, chain A (#2), sequence alignment
score = 570.2
RMSD between 195 pruned atom pairs is 0.869 angstroms; (across all 240 pairs:
2.475)
> rainbow structures palette cornflowerblue:red:gold
> ~display
> show :138 :< 5
> color byatom
> color :138 gold
> style stick
Changed 4119 atom styles
> view /a:138 :< 2
> hbonds :138
8 hydrogen bonds found
> transparency 90 target r
executed test.cxc
> ~hbonds
> hbonds :138!@C,N,O
Expected a keyword
> hbonds :138& @C,N,O
8 hydrogen bonds found
> hbonds :138 & !@C,N,O
Expected a keyword
> ~hbonds
> select up
Nothing selected
> select up
Nothing selected
> select up
Nothing selected
> hbonds :138& @C,N,O
8 hydrogen bonds found
> ~hbonds
> hbonds :138& !@C,N,O
Expected a keyword
> hbonds :138 & !@C,N,O
Expected a keyword
> hbonds :138 & sidechain
0 hydrogen bonds found
> hbonds :136 & sidechain
23 hydrogen bonds found
> help color
> rainbow :138 :< 5 target residues
> rainbow :138 :< 5 residues
> clsoe
Unknown command: clsoe
> close
> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/alexB/chimerax/test.cxc"
> open 1WMB 3U09
1wmb title:
Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more
info...]
Chain information for 1wmb #1
---
Chain | Description
A B | D(-)-3-hydroxybutyrate dehydrogenase
Non-standard residues in 1wmb #1
---
CAC — cacodylate ion (dimethylarsinate)
MG — magnesium ion
1wmb mmCIF Assemblies
---
1| author_and_software_defined_assembly
3u09 title:
Crystal structure of 3-ketoacyl-(acyl-carrier-protein) reductase (FabG)(G92D)
from Vibrio cholerae [more info...]
Chain information for 3u09 #2
---
Chain | Description
A B | 3-oxoacyl-[acyl-carrier-protein] reductase FabG
Non-standard residues in 3u09 #2
---
SO4 — sulfate ion
UNX — unknown atom or ion
3u09 mmCIF Assemblies
---
1| author_and_software_defined_assembly
> delete ~/a
> mmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1wmb, chain A (#1) with 3u09, chain A (#2), sequence alignment
score = 570.2
RMSD between 195 pruned atom pairs is 0.869 angstroms; (across all 240 pairs:
2.475)
> rainbow structures palette cornflowerblue:red:gold
> rainbow :138 :< 5 residues
> ~display
> show :138 :< 5
> color byatom
> color :138 gold
> style stick
Changed 4119 atom styles
> view /a:138 :< 2
> hbonds :138 & sidechain
0 hydrogen bonds found
> transparency 90 target r
executed test.cxc
> rainbow :138 :< 5 residues
> rainbow residues
> color grey
> rainbow residues
> rainbow target residue
> rainbow level residues
> rainbow level residues
> close
> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/alexB/chimerax/test.cxc"
> open 1WMB 3U09
1wmb title:
Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more
info...]
Chain information for 1wmb #1
---
Chain | Description
A B | D(-)-3-hydroxybutyrate dehydrogenase
Non-standard residues in 1wmb #1
---
CAC — cacodylate ion (dimethylarsinate)
MG — magnesium ion
1wmb mmCIF Assemblies
---
1| author_and_software_defined_assembly
3u09 title:
Crystal structure of 3-ketoacyl-(acyl-carrier-protein) reductase (FabG)(G92D)
from Vibrio cholerae [more info...]
Chain information for 3u09 #2
---
Chain | Description
A B | 3-oxoacyl-[acyl-carrier-protein] reductase FabG
Non-standard residues in 3u09 #2
---
SO4 — sulfate ion
UNX — unknown atom or ion
3u09 mmCIF Assemblies
---
1| author_and_software_defined_assembly
> delete ~/a
> mmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1wmb, chain A (#1) with 3u09, chain A (#2), sequence alignment
score = 570.2
RMSD between 195 pruned atom pairs is 0.869 angstroms; (across all 240 pairs:
2.475)
> rainbow structures palette cornflowerblue:red:gold
> ~display
> show :138 :< 5
> color byatom
> color :138 gold
> style stick
Changed 4119 atom styles
> view /a:138 :< 2
> hbonds :138 & sidechain
0 hydrogen bonds found
> transparency 90 target r
executed test.cxc
> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/alexB/chimerax/test.cxc"
> close
> open 1WMB 3U09
1wmb title:
Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more
info...]
Chain information for 1wmb #1
---
Chain | Description
A B | D(-)-3-hydroxybutyrate dehydrogenase
Non-standard residues in 1wmb #1
---
CAC — cacodylate ion (dimethylarsinate)
MG — magnesium ion
1wmb mmCIF Assemblies
---
1| author_and_software_defined_assembly
3u09 title:
Crystal structure of 3-ketoacyl-(acyl-carrier-protein) reductase (FabG)(G92D)
from Vibrio cholerae [more info...]
Chain information for 3u09 #2
---
Chain | Description
A B | 3-oxoacyl-[acyl-carrier-protein] reductase FabG
Non-standard residues in 3u09 #2
---
SO4 — sulfate ion
UNX — unknown atom or ion
3u09 mmCIF Assemblies
---
1| author_and_software_defined_assembly
> delete ~/a
> mmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1wmb, chain A (#1) with 3u09, chain A (#2), sequence alignment
score = 570.2
RMSD between 195 pruned atom pairs is 0.869 angstroms; (across all 240 pairs:
2.475)
> rainbow structures palette cornflowerblue:red:gold
> ~display
> show :138 :< 5
> color byatom
> color :138 gold
> style stick
Changed 4119 atom styles
> view /a:138 :< 2
> hbonds :138 & sidechain
0 hydrogen bonds found
> transparency 90 target r
executed test.cxc
> view :138
> view :138
> close
> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/alexB/chimerax/test.cxc"
> close
> open 1WMB 3U09
1wmb title:
Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more
info...]
Chain information for 1wmb #1
---
Chain | Description
A B | D(-)-3-hydroxybutyrate dehydrogenase
Non-standard residues in 1wmb #1
---
CAC — cacodylate ion (dimethylarsinate)
MG — magnesium ion
1wmb mmCIF Assemblies
---
1| author_and_software_defined_assembly
3u09 title:
Crystal structure of 3-ketoacyl-(acyl-carrier-protein) reductase (FabG)(G92D)
from Vibrio cholerae [more info...]
Chain information for 3u09 #2
---
Chain | Description
A B | 3-oxoacyl-[acyl-carrier-protein] reductase FabG
Non-standard residues in 3u09 #2
---
SO4 — sulfate ion
UNX — unknown atom or ion
3u09 mmCIF Assemblies
---
1| author_and_software_defined_assembly
> delete ~/a
> mmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1wmb, chain A (#1) with 3u09, chain A (#2), sequence alignment
score = 570.2
RMSD between 195 pruned atom pairs is 0.869 angstroms; (across all 240 pairs:
2.475)
> rainbow structures palette cornflowerblue:red:gold
> ~display
> show :138 :< 5
> color byatom
> color :138 gold
> style stick
Changed 4119 atom styles
> view /a:138
> hbonds :138 & sidechain
0 hydrogen bonds found
> transparency 90 target r
executed test.cxc
> help zone
> ~display
> display :138 :< 5 & sidechain
> display :138 :< 5
> ~display
> display :138 :< 5 & sidechain
> ~display
> display :138 :< 5 & @CB
> display :138 @< 5
> display :138 < 5
> show :138 < 5
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> display :138 :< 5
> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/alexB/chimerax/test.cxc"
> close
> open 1WMB 3U09
1wmb title:
Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more
info...]
Chain information for 1wmb #1
---
Chain | Description
A B | D(-)-3-hydroxybutyrate dehydrogenase
Non-standard residues in 1wmb #1
---
CAC — cacodylate ion (dimethylarsinate)
MG — magnesium ion
1wmb mmCIF Assemblies
---
1| author_and_software_defined_assembly
3u09 title:
Crystal structure of 3-ketoacyl-(acyl-carrier-protein) reductase (FabG)(G92D)
from Vibrio cholerae [more info...]
Chain information for 3u09 #2
---
Chain | Description
A B | 3-oxoacyl-[acyl-carrier-protein] reductase FabG
Non-standard residues in 3u09 #2
---
SO4 — sulfate ion
UNX — unknown atom or ion
3u09 mmCIF Assemblies
---
1| author_and_software_defined_assembly
> delete ~/a
> mmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1wmb, chain A (#1) with 3u09, chain A (#2), sequence alignment
score = 570.2
RMSD between 195 pruned atom pairs is 0.869 angstroms; (across all 240 pairs:
2.475)
> rainbow structures palette cornflowerblue:red:gold
> ~display
> show :138 :< 5
> color byatom
> color :138 gold
> style stick
Changed 4119 atom styles
> view /a:138
> hbonds :138 & sidechain
0 hydrogen bonds found
> transparency 90 target r
executed test.cxc
> alias 138 :138 :<
> ~display
> display 138
> show 138
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> alias 138 :138 :<
> display 138
> show 138
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> alias 138 disp :138 :<
> 138
> show :138 :<
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/alexB/chimerax/test.cxc"
> close
> open 1WMB 3U09 3I3O 3IJR
1wmb title:
Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more
info...]
Chain information for 1wmb #1
---
Chain | Description
A B | D(-)-3-hydroxybutyrate dehydrogenase
Non-standard residues in 1wmb #1
---
CAC — cacodylate ion (dimethylarsinate)
MG — magnesium ion
1wmb mmCIF Assemblies
---
1| author_and_software_defined_assembly
3u09 title:
Crystal structure of 3-ketoacyl-(acyl-carrier-protein) reductase (FabG)(G92D)
from Vibrio cholerae [more info...]
Chain information for 3u09 #2
---
Chain | Description
A B | 3-oxoacyl-[acyl-carrier-protein] reductase FabG
Non-standard residues in 3u09 #2
---
SO4 — sulfate ion
UNX — unknown atom or ion
3u09 mmCIF Assemblies
---
1| author_and_software_defined_assembly
3i3o title:
2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from
Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more
info...]
Chain information for 3i3o #3
---
Chain | Description
A B C D E F G H | Short chain dehydrogenase
Non-standard residues in 3i3o #3
---
CAC — cacodylate ion (dimethylarsinate)
CL — chloride ion
MG — magnesium ion
NAE — nicotinamide adenine dinucleotide acetone adduct
3i3o mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3ijr title:
2.05 Angstrom resolution crystal structure of a short chain dehydrogenase from
Bacillus anthracis str. 'Ames Ancestor' in complex with NAD+ [more info...]
Chain information for 3ijr #4
---
Chain | Description
A B C D E F G H | Oxidoreductase, short chain dehydrogenase/reductase family
Non-standard residues in 3ijr #4
---
MG — magnesium ion
NAD — nicotinamide-adenine-dinucleotide
SO4 — sulfate ion
3ijr mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> delete ~/a
> mmaker #2,3,4 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1wmb, chain A (#1) with 3u09, chain A (#2), sequence alignment
score = 570.2
RMSD between 195 pruned atom pairs is 0.869 angstroms; (across all 240 pairs:
2.475)
Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#3), sequence alignment
score = 499.7
RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs:
3.736)
Matchmaker 1wmb, chain A (#1) with 3ijr, chain A (#4), sequence alignment
score = 517.6
RMSD between 190 pruned atom pairs is 0.951 angstroms; (across all 245 pairs:
3.106)
> rainbow structures palette cornflowerblue:red:gold
> ~display
> color byatom
> show #1,2:138 :< 5
> show #3,4:176 :< 5
> color #1,2:138 #3,4:176 gold
> style stick
Changed 8885 atom styles
> view #1,2:138
> hbonds #1,2:138 & sidechain
0 hydrogen bonds found
> transparency 90 target r
executed test.cxc
> ribbon
> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/alexB/chimerax/test.cxc"
> close
> open 1WMB 3U09 3I3O 3IJR
1wmb title:
Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more
info...]
Chain information for 1wmb #1
---
Chain | Description
A B | D(-)-3-hydroxybutyrate dehydrogenase
Non-standard residues in 1wmb #1
---
CAC — cacodylate ion (dimethylarsinate)
MG — magnesium ion
1wmb mmCIF Assemblies
---
1| author_and_software_defined_assembly
3u09 title:
Crystal structure of 3-ketoacyl-(acyl-carrier-protein) reductase (FabG)(G92D)
from Vibrio cholerae [more info...]
Chain information for 3u09 #2
---
Chain | Description
A B | 3-oxoacyl-[acyl-carrier-protein] reductase FabG
Non-standard residues in 3u09 #2
---
SO4 — sulfate ion
UNX — unknown atom or ion
3u09 mmCIF Assemblies
---
1| author_and_software_defined_assembly
3i3o title:
2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from
Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more
info...]
Chain information for 3i3o #3
---
Chain | Description
A B C D E F G H | Short chain dehydrogenase
Non-standard residues in 3i3o #3
---
CAC — cacodylate ion (dimethylarsinate)
CL — chloride ion
MG — magnesium ion
NAE — nicotinamide adenine dinucleotide acetone adduct
3i3o mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3ijr title:
2.05 Angstrom resolution crystal structure of a short chain dehydrogenase from
Bacillus anthracis str. 'Ames Ancestor' in complex with NAD+ [more info...]
Chain information for 3ijr #4
---
Chain | Description
A B C D E F G H | Oxidoreductase, short chain dehydrogenase/reductase family
Non-standard residues in 3ijr #4
---
MG — magnesium ion
NAD — nicotinamide-adenine-dinucleotide
SO4 — sulfate ion
3ijr mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> delete ~/a
> mmaker #2,3,4 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1wmb, chain A (#1) with 3u09, chain A (#2), sequence alignment
score = 570.2
RMSD between 195 pruned atom pairs is 0.869 angstroms; (across all 240 pairs:
2.475)
Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#3), sequence alignment
score = 499.7
RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs:
3.736)
Matchmaker 1wmb, chain A (#1) with 3ijr, chain A (#4), sequence alignment
score = 517.6
RMSD between 190 pruned atom pairs is 0.951 angstroms; (across all 245 pairs:
3.106)
> rainbow structures palette cornflowerblue:red:gold
> ~display
> ribbon
> color byatom
> show #1,2:138 :< 5
> show #3,4:176 :< 5
> color #1,2:138 #3,4:176 gold
> style stick
Changed 8885 atom styles
> view #1,2:138
> hbonds #1,2:138 & sidechain
0 hydrogen bonds found
> transparency 90 target r
executed test.cxc
> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc"
> close
> graphics bgColor white
> open 1WMB
1wmb title:
Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more
info...]
Chain information for 1wmb #1
---
Chain | Description
A B | D(-)-3-hydroxybutyrate dehydrogenase
Non-standard residues in 1wmb #1
---
CAC — cacodylate ion (dimethylarsinate)
MG — magnesium ion
1wmb mmCIF Assemblies
---
1| author_and_software_defined_assembly
> open 3I3O
3i3o title:
2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from
Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more
info...]
Chain information for 3i3o #2
---
Chain | Description
A B C D E F G H | Short chain dehydrogenase
Non-standard residues in 3i3o #2
---
CAC — cacodylate ion (dimethylarsinate)
CL — chloride ion
MG — magnesium ion
NAE — nicotinamide adenine dinucleotide acetone adduct
3i3o mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> delete ~/a
> delete solvent
> mmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment
score = 499.7
RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs:
3.736)
> color #1 green
> color #2 tan
> color ~C byatom
> ~display
> display #1:138 #2:176
> style stick
Changed 4099 atom styles
> ribbon
> transparency 60 target r
> view
> size #1:138 #2:176 stickRadius 0.3
Changed 14 bond radii
> ~select
Nothing selected
> save fig1.jpg
> select #1@ca & #1:138@ca @< 7.5
13 atoms, 1 model selected
> select #1,2 & sel :< 2
204 atoms, 197 bonds, 2 models selected
> display sel
> color ~C byatom
> style stick
Changed 4099 atom styles
> view #1:138 :< 5 pad -1
> hbonds #1:138 & #1
3 hydrogen bonds found
> hbonds #2:176 & #2
4 hydrogen bonds found
> transparency 90 target r
> label #1:138 #2:176 offset 1,-1,1
> 2dlabels text 1WMB color green size 50 xpos .03 ypos .92
> 2dlabels text 3I3O color tan size 50 xpos .03 ypos .82
> label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1.5,2
> color green bgColor white
> label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1,1
> color tan bgColor white
> ~select
Nothing selected
> save fig2.jpg
> ~ribbon
> size stickRadius 0.05
Changed 4167 bond radii
> size #1:138 stickRadius 0.2
Changed 7 bond radii
> size #2:176 stickRadius 0.2
Changed 7 bond radii
> save fig3.jpg
> turn x 90
> save fig4.jpg
> turn y 90
> save fig5.jpg
> label #1:138 :< 5 & #1 height 0.4 offset 0,0,0 color green bgColor white
> label #2:176 :< 5 & #2 height 0.4 offset 0,1,0 color tan bgColor white
> view #1:138 :< 5 pad -1
> ~select
Nothing selected
> save fig6.jpg
> select #1@ca & #1:138@ca @< 7.5
13 atoms, 1 model selected
> select #1,2@ca & sel @< 2
26 atoms, 2 models selected
> align #2 & sel toAtoms #1 & sel
RMSD between 13 atom pairs is 0.455 angstroms
> ~select
Nothing selected
> save fig7.jpg
> select #1@ca & #1:138@ca @< 7.5
13 atoms, 1 model selected
> select #1,2 & sel :< 2
196 atoms, 189 bonds, 4 pseudobonds, 3 models selected
> ribbon sel
> ~select
Nothing selected
> save fig8.jpg
executed script.view.cxc
> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc"
> close
> graphics bgColor white
> open 1WMB
1wmb title:
Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more
info...]
Chain information for 1wmb #1
---
Chain | Description
A B | D(-)-3-hydroxybutyrate dehydrogenase
Non-standard residues in 1wmb #1
---
CAC — cacodylate ion (dimethylarsinate)
MG — magnesium ion
1wmb mmCIF Assemblies
---
1| author_and_software_defined_assembly
> open 3I3O
3i3o title:
2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from
Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more
info...]
Chain information for 3i3o #2
---
Chain | Description
A B C D E F G H | Short chain dehydrogenase
Non-standard residues in 3i3o #2
---
CAC — cacodylate ion (dimethylarsinate)
CL — chloride ion
MG — magnesium ion
NAE — nicotinamide adenine dinucleotide acetone adduct
3i3o mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> delete ~/a
> delete solvent
> mmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment
score = 499.7
RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs:
3.736)
> color #1 green
> color #2 tan
> color ~C byatom
> ~display
> display #1:138 #2:176
> style stick
Changed 4099 atom styles
> ribbon
> transparency 60 target r
> view
> size #1:138 #2:176 stickRadius 0.3
Changed 14 bond radii
> ~select
Nothing selected
> save fig1.jpg
> select #1@ca & #1:138@ca @< 7.5
13 atoms, 1 model selected
> select #1,2 & sel :< 2
204 atoms, 197 bonds, 2 models selected
> display sel
> color ~C byatom
> style stick
Changed 4099 atom styles
> view #1:138 :< 5 pad -1
> hbonds #1:138 & #1
3 hydrogen bonds found
> hbonds #2:176 & #2
4 hydrogen bonds found
> transparency 90 target r
> label #1:138 #2:176 offset 1,-1,1
> 2dlabels text 1WMB color green size 50 xpos .03 ypos .92
> 2dlabels text 3I3O color tan size 50 xpos .03 ypos .82
> label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1.5,2
> color green bgColor white
> label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1,1
> color tan bgColor white
> ~select
Nothing selected
> save fig2.jpg
> ~ribbon
> size stickRadius 0.05
Changed 4167 bond radii
> size #1:138 stickRadius 0.2
Changed 7 bond radii
> size #2:176 stickRadius 0.2
Changed 7 bond radii
> save fig3.jpg
> turn x 90
> save fig4.jpg
> turn y 90
> save fig5.jpg
> label #1:138 :< 5 & #1 height 0.4 offset 0,0,0 color green bgColor white
> label #2:176 :< 5 & #2 height 0.4 offset 0,1,0 color tan bgColor white
> view #1:138 :< 5 pad -1
> ~select
Nothing selected
> save fig6.jpg
> select #1@ca & #1:138@ca @< 7.5
13 atoms, 1 model selected
> select #1,2@ca & sel @< 2
26 atoms, 2 models selected
> align #2 & sel toAtoms #1 & sel
RMSD between 13 atom pairs is 0.455 angstroms
> ~select
Nothing selected
> save fig7.jpg
> select #1@ca & #1:138@ca @< 7.5
13 atoms, 1 model selected
> select #1,2 & sel :< 2
196 atoms, 189 bonds, 4 pseudobonds, 3 models selected
> ribbon sel
> ~select
Nothing selected
> save fig8.jpg
executed script.view.cxc
> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc"
> close
> graphics bgColor white
> open 1WMB
1wmb title:
Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more
info...]
Chain information for 1wmb #1
---
Chain | Description
A B | D(-)-3-hydroxybutyrate dehydrogenase
Non-standard residues in 1wmb #1
---
CAC — cacodylate ion (dimethylarsinate)
MG — magnesium ion
1wmb mmCIF Assemblies
---
1| author_and_software_defined_assembly
> open 3I3O
3i3o title:
2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from
Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more
info...]
Chain information for 3i3o #2
---
Chain | Description
A B C D E F G H | Short chain dehydrogenase
Non-standard residues in 3i3o #2
---
CAC — cacodylate ion (dimethylarsinate)
CL — chloride ion
MG — magnesium ion
NAE — nicotinamide adenine dinucleotide acetone adduct
3i3o mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> delete ~/a
> delete solvent
> mmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment
score = 499.7
RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs:
3.736)
> color #1 green
> color #2 tan
> color ~C byatom
> ~display
> display #1:138 #2:176
> style stick
Changed 4099 atom styles
> ribbon
> transparency 60 target r
> view
> size #1:138 #2:176 stickRadius 0.3
Changed 14 bond radii
> ~select
Nothing selected
> save fig1.jpg
> select #1@ca & #1:138@ca @< 7.5
13 atoms, 1 model selected
> select #1,2 & sel :< 2
204 atoms, 197 bonds, 2 models selected
> display sel
> color ~C byatom
> style stick
Changed 4099 atom styles
> view #1:138 :< 5 pad -1
> hbonds #1:138 & #1
3 hydrogen bonds found
> hbonds #2:176 & #2
4 hydrogen bonds found
> transparency 90 target r
> label #1:138 #2:176 offset 1,-1,1
> 2dlabels text 1WMB color green size 50 xpos .03 ypos .92
> 2dlabels text 3I3O color tan size 50 xpos .03 ypos .82
> label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1.5,2
> color green bgColor white
> label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1,1
> color tan bgColor white
> ~select
Nothing selected
> save fig2.jpg
> ~ribbon
> size stickRadius 0.05
Changed 4167 bond radii
> size #1:138 stickRadius 0.2
Changed 7 bond radii
> size #2:176 stickRadius 0.2
Changed 7 bond radii
> save fig3.jpg
> turn x 90
> save fig4.jpg
> turn y 90
> save fig5.jpg
> label #1:138 :< 5 & #1 height 0.4 offset 0,0,0 color green bgColor white
> label #2:176 :< 5 & #2 height 0.4 offset 0,1,0 color tan bgColor white
> view #1:138 :< 5 pad -1
> ~select
Nothing selected
> save fig6.jpg
> select #1@ca & #1:138@ca @< 7.5
13 atoms, 1 model selected
> select #1,2@ca & sel @< 2
26 atoms, 2 models selected
> align #2 & sel toAtoms #1 & sel
RMSD between 13 atom pairs is 0.455 angstroms
> ~select
Nothing selected
> save fig7.jpg
> select #1@ca & #1:138@ca @< 7.5
13 atoms, 1 model selected
> select #1,2 & sel :< 1
196 atoms, 189 bonds, 4 pseudobonds, 3 models selected
> ribbon sel
> ~select
Nothing selected
> save fig8.jpg
executed script.view.cxc
> style @ca sphere
Changed 542 atom styles
> select #1/A:89@CA
1 atom, 1 model selected
> distance #1/A:89@CA #2/A:129@CA
Distance between 1wmb #1/A ASN 89 CA and 3i3o #2/A ASN 129 CA: 3.719Å
> select clear
> select #2/A:128@CA
1 atom, 1 model selected
> distance #2/A:128@CA #2/A:129@CA
Distance between 3i3o #2/A ASN 128 CA and ASN 129 CA: 3.769Å
> select clear
> select #1/A:89@CA
1 atom, 1 model selected
> distance #1/A:89@CA #2/A:129@CA
Distance already exists; modify distance properties with 'distance style'
> hide #5.1 models
> select clear
> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc"
> close
> graphics bgColor white
> open 1WMB
1wmb title:
Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more
info...]
Chain information for 1wmb #1
---
Chain | Description
A B | D(-)-3-hydroxybutyrate dehydrogenase
Non-standard residues in 1wmb #1
---
CAC — cacodylate ion (dimethylarsinate)
MG — magnesium ion
1wmb mmCIF Assemblies
---
1| author_and_software_defined_assembly
> open 3I3O
3i3o title:
2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from
Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more
info...]
Chain information for 3i3o #2
---
Chain | Description
A B C D E F G H | Short chain dehydrogenase
Non-standard residues in 3i3o #2
---
CAC — cacodylate ion (dimethylarsinate)
CL — chloride ion
MG — magnesium ion
NAE — nicotinamide adenine dinucleotide acetone adduct
3i3o mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> delete ~/a
> delete solvent
> mmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment
score = 499.7
RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs:
3.736)
> color #1 green
> color #2 tan
> color ~C byatom
> ~display
> display #1:138 #2:176
> style stick
Changed 4099 atom styles
> ribbon
> transparency 60 target r
> view
> size #1:138 #2:176 stickRadius 0.3
Changed 14 bond radii
> ~select
Nothing selected
> save fig1.jpg
> select #1@ca & #1:138@ca @< 7.5
13 atoms, 1 model selected
> select #1,2 & sel :< 1
185 atoms, 177 bonds, 2 models selected
> display sel
> color ~C byatom
> style stick
Changed 4099 atom styles
> view #1:138 :< 5 pad -1
> hbonds #1:138 & #1
3 hydrogen bonds found
> hbonds #2:176 & #2
4 hydrogen bonds found
> transparency 90 target r
> label #1:138 #2:176 offset 1,-1,1
> 2dlabels text 1WMB color green size 50 xpos .03 ypos .92
> 2dlabels text 3I3O color tan size 50 xpos .03 ypos .82
> label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1.5,2
> color green bgColor white
> label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1,1
> color tan bgColor white
> ~select
Nothing selected
> save fig2.jpg
> ~ribbon
> size stickRadius 0.05
Changed 4167 bond radii
> size #1:138 stickRadius 0.2
Changed 7 bond radii
> size #2:176 stickRadius 0.2
Changed 7 bond radii
> save fig3.jpg
> label #1:138 :< 5 & #1 height 0.4 offset 0,0,0 color green bgColor white
> label #2:176 :< 5 & #2 height 0.4 offset 0,1,0 color tan bgColor white
> view #1:138 :< 5 pad -1
> ~select
Nothing selected
> save fig4.jpg
> select #1@ca & #1:138@ca @< 7.5
13 atoms, 1 model selected
> select #1,2@ca & sel @< 1
24 atoms, 2 models selected
> align #2 & sel toAtoms #1 & sel
Unequal number of atoms to pair, 11 and 13
> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc"
> close
> graphics bgColor white
> open 1WMB
1wmb title:
Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more
info...]
Chain information for 1wmb #1
---
Chain | Description
A B | D(-)-3-hydroxybutyrate dehydrogenase
Non-standard residues in 1wmb #1
---
CAC — cacodylate ion (dimethylarsinate)
MG — magnesium ion
1wmb mmCIF Assemblies
---
1| author_and_software_defined_assembly
> open 3I3O
3i3o title:
2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from
Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more
info...]
Chain information for 3i3o #2
---
Chain | Description
A B C D E F G H | Short chain dehydrogenase
Non-standard residues in 3i3o #2
---
CAC — cacodylate ion (dimethylarsinate)
CL — chloride ion
MG — magnesium ion
NAE — nicotinamide adenine dinucleotide acetone adduct
3i3o mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> delete ~/a
> delete solvent
> mmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment
score = 499.7
RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs:
3.736)
[had to truncate log due to ticket-length limitation]
> sel-ca
13 atoms, 1 model selected
26 atoms, 2 models selected
> ~ribbon
> size stickRadius 0.05
Changed 4167 bond radii
> size #1:138 stickRadius 0.2
Changed 7 bond radii
> size #2:176 stickRadius 0.2
Changed 7 bond radii
> view sel-residues pad -1
> ~select
Nothing selected
> save fig3.jpg
> sel-ca
13 atoms, 1 model selected
26 atoms, 2 models selected
> view sel-residues pad -1
> sel-ca
13 atoms, 1 model selected
26 atoms, 2 models selected
> align #2 & sel toAtoms #1 & sel
RMSD between 13 atom pairs is 0.455 angstroms
> ~select
Nothing selected
> save fig4.jpg
> sel-ca
13 atoms, 1 model selected
26 atoms, 2 models selected
> ribbon sel
> ~select
Nothing selected
> save fig5.jpg
> sel-ca
13 atoms, 1 model selected
26 atoms, 2 models selected
> label sel-residues text "{0.name} {0.number} {0.phi:.1f},{0.psi:.1f}" height
> 0.5 color green bgColor white offset 0,0,0
> label sel-residues text "{0.name} {0.number} {0.phi:.1f},{0.psi:.1f}" height
> 0.5 color tan bgColor white offset 0,0.7,0
> ~select
Nothing selected
No known data format for file suffix '.jpb'
> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc"
> close
> graphics bgColor white
> open 1WMB
1wmb title:
Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more
info...]
Chain information for 1wmb #1
---
Chain | Description
A B | D(-)-3-hydroxybutyrate dehydrogenase
Non-standard residues in 1wmb #1
---
CAC — cacodylate ion (dimethylarsinate)
MG — magnesium ion
1wmb mmCIF Assemblies
---
1| author_and_software_defined_assembly
> open 3I3O
3i3o title:
2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from
Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more
info...]
Chain information for 3i3o #2
---
Chain | Description
A B C D E F G H | Short chain dehydrogenase
Non-standard residues in 3i3o #2
---
CAC — cacodylate ion (dimethylarsinate)
CL — chloride ion
MG — magnesium ion
NAE — nicotinamide adenine dinucleotide acetone adduct
3i3o mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> delete ~/a
> delete solvent
> mmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment
score = 499.7
RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs:
3.736)
> color #1 green
> color #2 tan
> color ~C byatom
> ~display
> display #1:138 #2:176
> style stick
Changed 4099 atom styles
> ribbon
> transparency 60 target r
> view
> size #1:138 #2:176 stickRadius 0.3
Changed 14 bond radii
> save fig1.jpg
> alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2
> sel-ca
13 atoms, 1 model selected
26 atoms, 2 models selected
> display sel-residues
> color ~C byatom
> style stick
Changed 4099 atom styles
> view #1:138 :< 5 pad -1
> hbonds #1:138 & #1 name hb1 color green
3 hydrogen bonds found
> hbonds #2:176 & #2 name hb2 color tan
4 hydrogen bonds found
> transparency 90 target r
> label #1:138 #2:176 offset 1,-1,1
> 2dlabels text 1WMB color green size 40 xpos .03 ypos .90
> 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82
> label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white
> label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white
> label #1:138 text "{0.name} {0.number} {0.phi:.1f},{0.psi:.1f}" height 0.5
> color green bgColor white offset 0,0,0
> label #2:176 text "{0.name} {0.number} {0.phi:.1f},{0.psi:.1f}" height 0.5
> color tan bgColor white offset 0,0.7,0
> ~select
Nothing selected
> save fig2.jpg
> sel-ca
13 atoms, 1 model selected
26 atoms, 2 models selected
> ~ribbon
> size stickRadius 0.05
Changed 4167 bond radii
> size #1:138 stickRadius 0.2
Changed 7 bond radii
> size #2:176 stickRadius 0.2
Changed 7 bond radii
> view sel-residues pad -1
> ~select
Nothing selected
> save fig3.jpg
> sel-ca
13 atoms, 1 model selected
26 atoms, 2 models selected
> view sel-residues pad -1
> sel-ca
13 atoms, 1 model selected
26 atoms, 2 models selected
> align #2 & sel toAtoms #1 & sel
RMSD between 13 atom pairs is 0.455 angstroms
> ~select
Nothing selected
> save fig4.jpg
> sel-ca
13 atoms, 1 model selected
26 atoms, 2 models selected
> ribbon sel
> ~select
Nothing selected
> save fig5.jpg
> sel-ca
13 atoms, 1 model selected
26 atoms, 2 models selected
> label sel-residues text "{0.name} {0.number} {0.phi:.1f},{0.psi:.1f}" height
> 0.5 color green bgColor white offset 0,0,0
> label sel-residues text "{0.name} {0.number} {0.phi:.1f},{0.psi:.1f}" height
> 0.5 color tan bgColor white offset 0,0.7,0
> ~select
Nothing selected
> save fig5b.jpg
executed script.view.cxc
> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc"
> close
> graphics bgColor white
> open 1WMB
1wmb title:
Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more
info...]
Chain information for 1wmb #1
---
Chain | Description
A B | D(-)-3-hydroxybutyrate dehydrogenase
Non-standard residues in 1wmb #1
---
CAC — cacodylate ion (dimethylarsinate)
MG — magnesium ion
1wmb mmCIF Assemblies
---
1| author_and_software_defined_assembly
> open 3I3O
3i3o title:
2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from
Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more
info...]
Chain information for 3i3o #2
---
Chain | Description
A B C D E F G H | Short chain dehydrogenase
Non-standard residues in 3i3o #2
---
CAC — cacodylate ion (dimethylarsinate)
CL — chloride ion
MG — magnesium ion
NAE — nicotinamide adenine dinucleotide acetone adduct
3i3o mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> delete ~/a
> delete solvent
> mmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment
score = 499.7
RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs:
3.736)
> color #1 green
> color #2 tan
> color ~C byatom
> ~display
> display #1:138 #2:176
> style stick
Changed 4099 atom styles
> ribbon
> transparency 60 target r
> view
> size #1:138 #2:176 stickRadius 0.3
Changed 14 bond radii
> save fig1.jpg
> alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2
> sel-ca
13 atoms, 1 model selected
26 atoms, 2 models selected
> display sel-residues
> color ~C byatom
> style stick
Changed 4099 atom styles
> view #1:138 :< 5 pad -1
> hbonds #1:138 & #1 name hb1 color green
3 hydrogen bonds found
> hbonds #2:176 & #2 name hb2 color tan
4 hydrogen bonds found
> transparency 90 target r
> label #1:138 #2:176 offset 1,-1,1
> 2dlabels text 1WMB color green size 40 xpos .03 ypos .90
> 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82
> label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white
> label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white
> label #1:138 text "{0.name} {0.number} {0.phi:.1f},{0.psi:.1f}" height 0.5
> color green bgColor white offset 0,0,0
> label #2:176 text "{0.name} {0.number} {0.phi:.1f},{0.psi:.1f}" height 0.5
> color tan bgColor white offset 0,0.7,0
> ~select
Nothing selected
> save fig2.jpg
> sel-ca
13 atoms, 1 model selected
26 atoms, 2 models selected
> ~ribbon
> size stickRadius 0.05
Changed 4167 bond radii
> size #1:138 stickRadius 0.2
Changed 7 bond radii
> size #2:176 stickRadius 0.2
Changed 7 bond radii
> view sel-residues pad -1
> ~select
Nothing selected
> save fig3.jpg
> sel-ca
13 atoms, 1 model selected
26 atoms, 2 models selected
> view sel-residues pad -1
> sel-ca
13 atoms, 1 model selected
26 atoms, 2 models selected
> align #2 & sel toAtoms #1 & sel
RMSD between 13 atom pairs is 0.455 angstroms
> ~select
Nothing selected
> save fig4.jpg
> sel-ca
13 atoms, 1 model selected
26 atoms, 2 models selected
> ribbon sel
> ~select
Nothing selected
> save fig5.jpg
> sel-ca
13 atoms, 1 model selected
26 atoms, 2 models selected
> label sel-residues & #1 text "{0.name} {0.number} {0.phi:.1f},{0.psi:.1f}"
> height 0.5 color green bgColor white offset 0,0,0
> label sel-residues & #2 text "{0.name} {0.number} {0.phi:.1f},{0.psi:.1f}"
> height 0.5 color tan bgColor white offset 0,0.7,0
> ~select
Nothing selected
> save fig5b.jpg
executed script.view.cxc
> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc"
> close
> graphics bgColor white
> open 1WMB
1wmb title:
Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more
info...]
Chain information for 1wmb #1
---
Chain | Description
A B | D(-)-3-hydroxybutyrate dehydrogenase
Non-standard residues in 1wmb #1
---
CAC — cacodylate ion (dimethylarsinate)
MG — magnesium ion
1wmb mmCIF Assemblies
---
1| author_and_software_defined_assembly
> open 3I3O
3i3o title:
2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from
Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more
info...]
Chain information for 3i3o #2
---
Chain | Description
A B C D E F G H | Short chain dehydrogenase
Non-standard residues in 3i3o #2
---
CAC — cacodylate ion (dimethylarsinate)
CL — chloride ion
MG — magnesium ion
NAE — nicotinamide adenine dinucleotide acetone adduct
3i3o mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> delete ~/a
> delete solvent
> mmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment
score = 499.7
RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs:
3.736)
> color #1 green
> color #2 tan
> color ~C byatom
> ~display
> display #1:138 #2:176
> style stick
Changed 4099 atom styles
> ribbon
> transparency 60 target r
> view
> size #1:138 #2:176 stickRadius 0.3
Changed 14 bond radii
> save fig1.jpg
> alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2
> sel-ca
13 atoms, 1 model selected
26 atoms, 2 models selected
> display sel-residues
> color ~C byatom
> style stick
Changed 4099 atom styles
> view #1:138 :< 5 pad -1
> hbonds #1:138 & #1 name hb1 color green
3 hydrogen bonds found
> hbonds #2:176 & #2 name hb2 color tan
4 hydrogen bonds found
> transparency 90 target r
> label #1:138 #2:176 offset 1,-1,1
> 2dlabels text 1WMB color green size 40 xpos .03 ypos .90
> 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82
> label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white
> label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white
> label #1:138 text "{0.name} {0.number} {0.phi:.1f},{0.psi:.1f}" height 0.5
> color green bgColor white offset 0,0,0
> label #2:176 text "{0.name} {0.number} {0.phi:.1f},{0.psi:.1f}" height 0.5
> color tan bgColor white offset 0,0.7,0
> ~select
Nothing selected
> save fig2.jpg
> sel-ca
13 atoms, 1 model selected
26 atoms, 2 models selected
> ~ribbon
> size stickRadius 0.05
Changed 4167 bond radii
> size #1:138 stickRadius 0.2
Changed 7 bond radii
> size #2:176 stickRadius 0.2
Changed 7 bond radii
> view sel-residues pad -1
> ~select
Nothing selected
> save fig3.jpg
> sel-ca
13 atoms, 1 model selected
26 atoms, 2 models selected
> view sel-residues pad -1
> sel-ca
13 atoms, 1 model selected
26 atoms, 2 models selected
> align #2 & sel toAtoms #1 & sel
RMSD between 13 atom pairs is 0.455 angstroms
> ~select
Nothing selected
> save fig4.jpg
> sel-ca
13 atoms, 1 model selected
26 atoms, 2 models selected
> ribbon sel
> ~select
Nothing selected
> save fig5.jpg
> sel-ca
13 atoms, 1 model selected
26 atoms, 2 models selected
> label sel-residues & #1 text "{0.name} {0.number} {0.phi:.1f},{0.psi:.1f}"
> height 0.4 color green bgColor white offset 0,0,0
> label sel-residues & #2 text "{0.name} {0.number} {0.phi:.1f},{0.psi:.1f}"
> height 0.4 color tan bgColor white offset 0,0.7,0
> ~select
Nothing selected
> save fig5b.jpg
executed script.view.cxc
> help ribbon
> cartoon style width 1.5 thickness 0.3
> cartoon style helix width 1.5 thickness 0.3
> cartoon style helix width 1.5 thickness 0.3
> cartoon style strand xsection rectangle width 2
> cartoon style width 1.5 thickness 0.3
> cartoon style width 1.5 thickness 0.2
> cartoon style width 1 thickness 0.2
> cartoon style width 0.8 thickness 0.2
> cartoon style width 0.8 thickness 0.1
> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc"
> close
> graphics bgColor white
> open 1WMB
1wmb title:
Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more
info...]
Chain information for 1wmb #1
---
Chain | Description
A B | D(-)-3-hydroxybutyrate dehydrogenase
Non-standard residues in 1wmb #1
---
CAC — cacodylate ion (dimethylarsinate)
MG — magnesium ion
1wmb mmCIF Assemblies
---
1| author_and_software_defined_assembly
> open 3I3O
3i3o title:
2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from
Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more
info...]
Chain information for 3i3o #2
---
Chain | Description
A B C D E F G H | Short chain dehydrogenase
Non-standard residues in 3i3o #2
---
CAC — cacodylate ion (dimethylarsinate)
CL — chloride ion
MG — magnesium ion
NAE — nicotinamide adenine dinucleotide acetone adduct
3i3o mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> delete ~/a
> delete solvent
> mmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment
score = 499.7
RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs:
3.736)
> color #1 green
> color #2 tan
> color ~C byatom
> ~display
> display #1:138 #2:176
> style stick
Changed 4099 atom styles
> ribbon
> transparency 60 target r
> view
> size #1:138 #2:176 stickRadius 0.3
Changed 14 bond radii
> save fig1.jpg
> alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2
> sel-ca
13 atoms, 1 model selected
26 atoms, 2 models selected
> display sel-residues
> color ~C byatom
> style stick
Changed 4099 atom styles
> view #1:138 :< 5 pad -1
> hbonds #1:138 & #1 name hb1 color green
3 hydrogen bonds found
> hbonds #2:176 & #2 name hb2 color tan
4 hydrogen bonds found
> transparency 90 target r
> label #1:138 #2:176 offset 1,-1,1
> 2dlabels text 1WMB color green size 40 xpos .03 ypos .90
> 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82
> label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white
> label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white
> label #1:138 text "{0.name} {0.number} {0.phi:.1f},{0.psi:.1f}" height 0.5
> color green bgColor white offset 0,0,0
> label #2:176 text "{0.name} {0.number} {0.phi:.1f},{0.psi:.1f}" height 0.5
> color tan bgColor white offset 0,0.7,0
> ~select
Nothing selected
> save fig2.jpg
> sel-ca
13 atoms, 1 model selected
26 atoms, 2 models selected
> ~ribbon
> size stickRadius 0.05
Changed 4167 bond radii
> size #1:138 stickRadius 0.2
Changed 7 bond radii
> size #2:176 stickRadius 0.2
Changed 7 bond radii
> view sel-residues pad -1
> ~select
Nothing selected
> save fig3.jpg
> sel-ca
13 atoms, 1 model selected
26 atoms, 2 models selected
> view sel-residues pad -1
> sel-ca
13 atoms, 1 model selected
26 atoms, 2 models selected
> align #2 & sel toAtoms #1 & sel
RMSD between 13 atom pairs is 0.455 angstroms
> ~select
Nothing selected
> save fig4.jpg
> sel-ca
13 atoms, 1 model selected
26 atoms, 2 models selected
> ribbon sel
> cartoon style width 1 thickness 0.2
> ~select
Nothing selected
> save fig5.jpg
executed script.view.cxc
> ~ribbon
> view
> ribbon
> surface #138
No atoms specified by #138
> surface #1:138
> surface #1:138~disp
Expected an atoms specifier or a keyword
> ~display
> ~hbonds
> ~label
> delete hbond
Missing or invalid "atoms" argument: invalid atoms specifier
> view
> surface #1:138 :/, 7.5
Expected a keyword
> surface #1:138 :< 7.5
> surface
> ~surface
> surface :138
> delete #2
> ~surface
> surface #138
No atoms specified by #138
> surface :138
> close #3-4#5
> close #1.1,3
> display :138
> surface :138
> display :138 :< 7.5
> close
> close
> graphics bgColor white
> open 1WMB
1wmb title:
Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more
info...]
Chain information for 1wmb #1
---
Chain | Description
A B | D(-)-3-hydroxybutyrate dehydrogenase
Non-standard residues in 1wmb #1
---
CAC — cacodylate ion (dimethylarsinate)
MG — magnesium ion
1wmb mmCIF Assemblies
---
1| author_and_software_defined_assembly
> open 3I3O
3i3o title:
2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from
Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more
info...]
Chain information for 3i3o #2
---
Chain | Description
A B C D E F G H | Short chain dehydrogenase
Non-standard residues in 3i3o #2
---
CAC — cacodylate ion (dimethylarsinate)
CL — chloride ion
MG — magnesium ion
NAE — nicotinamide adenine dinucleotide acetone adduct
3i3o mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> delete ~/a
> delete solvent
> mmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment
score = 499.7
RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs:
3.736)
> color #1 green
> color #2 tan
> color ~C byatom
> ~display
> display #1:138 #2:176
> style stick
Changed 4099 atom styles
> ribbon
> transparency 60 target r
> view
> size #1:138 #2:176 stickRadius 0.3
Changed 14 bond radii
> display #1:138 :< 7.5
> ~display
> display #1:138 @< 7.5
> ~display
> display #1:138@ca @< 7.5
> display #1:138@ca @ca< 7.5
> show #1:138@ca @ca< 7.5
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> display #1:138@ca @< 7.5 & @ca
> ~display
> display #1:138@ca @< 7.5 & @ca
> ~ribbon #1:138@ca @< 7.5 & @ca
> display sel-residues
> ~ribbon #1:138@ca @< 7.5 & @ca
> display sel-residues
> display #1:138@ca @< 7.5 & @ca
> display sel-residues
> select #1:138@ca @< 7.5 & @ca
28 atoms, 19 pseudobonds, 4 models selected
> display sel-residues
> ribbon
> select clear
> help residues
No help found for 'residues'
> help surface
> surface style meshe
Missing or invalid "style" argument: Should be one of 'dot', 'mesh', or
'solid'
> surface style mesh
> surface sel-residues
No atoms specified by sel-residues
> select #1:138@ca @< 7.5 & @ca
28 atoms, 2 models selected
> surface sel-residues
> surface style mesh
> ~ribbon
> surface sel-residues enclose sel-residues
> select clear
> ribbon
> transparency 50 target s
> transparency 50 target r
> transparency 90 target r
> transparency 70 target r
> color blue target s
> transparency 50 target s
> transparency 80 target s
> ~display
> display #1:138
> display #2:176
> save "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/alexB/chimerax/test_surf.jpg" width 1963 height 1218
> supersample 3
> transparency 50 target s
> transparency 90 target s
> surface style mesh
> transparency 00 target s
> transparency 20 target s
> transparency 30 target s
> transparency 40 target s
> transparency 90 target s
> transparency 70 target s
> surface style dot
> surface style mesh
> save "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/alexB/chimerax/test_surf2.jpg" width 1963 height 1218
> supersample 3
> surface style solid
> transparency 950 target s
> transparency 95 target s
> save "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/alexB/chimerax/test_surf3.jpg" width 1963 height 1218
> supersample 3
> surface #2:176 :< 7.5 enclose #2:176 :< 7.5
> transparency 950 target s
> transparency 95 target s
> hide #3 models
> show #3 models
> transparency 55 target s
> surface #2:176 :< 7.5 & #1enclose #2:176 :< 7.5
Expected a keyword
> surface #2:176 :< 7.5 & #2 enclose #2:176 :< 7.5
> hide #3 models
> show #3 models
> close
> open "/Users/admin/Dropbox (Technion Dropbox)/PROJECTS/andrewL/SEC7domain-
> hhpred/SEQ7_hhpred_modeller_5NLY_A.pdb"
Chain information for SEQ7_hhpred_modeller_5NLY_A.pdb #1
---
Chain | Description
X | No description available
> open "/Users/admin/Dropbox (Technion Dropbox)/PROJECTS/andrewL/pydock/IQ-
> motif-M1/project13584_2771.pdb"
Summary of feedback from opening /Users/admin/Dropbox (Technion
Dropbox)/PROJECTS/andrewL/pydock/IQ-motif-M1/project13584_2771.pdb
---
warnings | Duplicate atom serial number found: 150
Duplicate atom serial number found: 151
Duplicate atom serial number found: 153
Duplicate atom serial number found: 155
Duplicate atom serial number found: 158
413 messages similar to the above omitted
Chain information for project13584_2771.pdb #2
---
Chain | Description
A | No description available
X | No description available
> open "/Users/admin/Dropbox (Technion Dropbox)/PROJECTS/andrewL/pydock/IQ-
> motif-M1/project13584_7702.pdb"
Summary of feedback from opening /Users/admin/Dropbox (Technion
Dropbox)/PROJECTS/andrewL/pydock/IQ-motif-M1/project13584_7702.pdb
---
warnings | Duplicate atom serial number found: 150
Duplicate atom serial number found: 151
Duplicate atom serial number found: 153
Duplicate atom serial number found: 155
Duplicate atom serial number found: 158
413 messages similar to the above omitted
Chain information for project13584_7702.pdb #3
---
Chain | Description
A | No description available
X | No description available
> ui tool show "Blast Protein"
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A #3/A
Alignment identifier is 1
Seqview [ID: 1] region 2 chains [28-30] RMSD: 27.880
> display sel
> hide #3 models
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A #3/A
Alignment identifier is 2
> ui tool show "Show Sequence Viewer"
> sequence chain #1/X #2/X #3/X
Alignment identifier is 3
Seqview [ID: 3] region 3 chains [85-87] RMSD: 0.000
> display sel
> select clear
> color /a:28-30 & C gold
> style sphere
Changed 9582 atom styles
> color /x:102-104 & C orange
> show #3 models
> open "/Users/admin/Dropbox (Technion Dropbox)/PROJECTS/andrewL/pydock/IQ-
> motif-M1/project13584_3168.pdb"
Summary of feedback from opening /Users/admin/Dropbox (Technion
Dropbox)/PROJECTS/andrewL/pydock/IQ-motif-M1/project13584_3168.pdb
---
warnings | Duplicate atom serial number found: 150
Duplicate atom serial number found: 151
Duplicate atom serial number found: 153
Duplicate atom serial number found: 155
Duplicate atom serial number found: 158
413 messages similar to the above omitted
Chain information for project13584_3168.pdb #4
---
Chain | Description
A | No description available
X | No description available
> show /x:102-104
> display /a:28-30
> style sphere
Changed 12942 atom styles
> open "/Users/admin/Dropbox (Technion Dropbox)/PROJECTS/andrewL/pydock/IQ-
> motif-M1/project13584_9644.pdb"
Summary of feedback from opening /Users/admin/Dropbox (Technion
Dropbox)/PROJECTS/andrewL/pydock/IQ-motif-M1/project13584_9644.pdb
---
warnings | Duplicate atom serial number found: 150
Duplicate atom serial number found: 151
Duplicate atom serial number found: 153
Duplicate atom serial number found: 155
Duplicate atom serial number found: 158
413 messages similar to the above omitted
Chain information for project13584_9644.pdb #5
---
Chain | Description
A | No description available
X | No description available
> style sphere
Changed 16302 atom styles
> display /a:28-30
> open "/Users/admin/Dropbox (Technion Dropbox)/PROJECTS/andrewL/pydock/IQ-
> motif-M1/project13584_6685.pdb"
Summary of feedback from opening /Users/admin/Dropbox (Technion
Dropbox)/PROJECTS/andrewL/pydock/IQ-motif-M1/project13584_6685.pdb
---
warnings | Duplicate atom serial number found: 150
Duplicate atom serial number found: 151
Duplicate atom serial number found: 153
Duplicate atom serial number found: 155
Duplicate atom serial number found: 158
413 messages similar to the above omitted
Chain information for project13584_6685.pdb #6
---
Chain | Description
A | No description available
X | No description available
> select up
Nothing selected
> display /a:28-30
> open "/Users/admin/Dropbox (Technion Dropbox)/PROJECTS/andrewL/pydock/IQ-
> motif-M1/project13584_77.pdb"
Summary of feedback from opening /Users/admin/Dropbox (Technion
Dropbox)/PROJECTS/andrewL/pydock/IQ-motif-M1/project13584_77.pdb
---
warnings | Duplicate atom serial number found: 150
Duplicate atom serial number found: 151
Duplicate atom serial number found: 153
Duplicate atom serial number found: 155
Duplicate atom serial number found: 158
413 messages similar to the above omitted
Chain information for project13584_77.pdb #7
---
Chain | Description
A | No description available
X | No description available
> display /a:28-30
> open "/Users/admin/Dropbox (Technion Dropbox)/PROJECTS/andrewL/pydock/IQ-
> motif-M1/project13584_4420.pdb"
Summary of feedback from opening /Users/admin/Dropbox (Technion
Dropbox)/PROJECTS/andrewL/pydock/IQ-motif-M1/project13584_4420.pdb
---
warnings | Duplicate atom serial number found: 150
Duplicate atom serial number found: 151
Duplicate atom serial number found: 153
Duplicate atom serial number found: 155
Duplicate atom serial number found: 158
413 messages similar to the above omitted
Chain information for project13584_4420.pdb #8
---
Chain | Description
A | No description available
X | No description available
> hide #7 models
> hide #6 models
> hide #5 models
> hide #4 models
> hide #3 models
> hide #2 models
> open "/Users/admin/Dropbox (Technion Dropbox)/PROJECTS/andrewL/pydock/IQ-
> motif-M1/project13584_7608.pdb"
Summary of feedback from opening /Users/admin/Dropbox (Technion
Dropbox)/PROJECTS/andrewL/pydock/IQ-motif-M1/project13584_7608.pdb
---
warnings | Duplicate atom serial number found: 150
Duplicate atom serial number found: 151
Duplicate atom serial number found: 153
Duplicate atom serial number found: 155
Duplicate atom serial number found: 158
413 messages similar to the above omitted
Chain information for project13584_7608.pdb #9
---
Chain | Description
A | No description available
X | No description available
> display /a:28-30
> open "/Users/admin/Dropbox (Technion Dropbox)/PROJECTS/andrewL/pydock/IQ-
> motif-M1/project13584_8585.pdb"
Summary of feedback from opening /Users/admin/Dropbox (Technion
Dropbox)/PROJECTS/andrewL/pydock/IQ-motif-M1/project13584_8585.pdb
---
warnings | Duplicate atom serial number found: 150
Duplicate atom serial number found: 151
Duplicate atom serial number found: 153
Duplicate atom serial number found: 155
Duplicate atom serial number found: 158
413 messages similar to the above omitted
Chain information for project13584_8585.pdb #10
---
Chain | Description
A | No description available
X | No description available
> display /a:28-30
> show #2 models
> show #3 models
> show #4 models
> show #5 models
> show #6 models
> show #7 models
> open "/Users/admin/Dropbox (Technion Dropbox)/PROJECTS/andrewL/pydock/IQ-
> motif-M1/project13584_1367.pdb"
Summary of feedback from opening /Users/admin/Dropbox (Technion
Dropbox)/PROJECTS/andrewL/pydock/IQ-motif-M1/project13584_1367.pdb
---
warnings | Duplicate atom serial number found: 150
Duplicate atom serial number found: 151
Duplicate atom serial number found: 153
Duplicate atom serial number found: 155
Duplicate atom serial number found: 158
413 messages similar to the above omitted
Chain information for project13584_1367.pdb #11
---
Chain | Description
A | No description available
X | No description available
> hide #2-10 target m
> display /a:28-30
> open "/Users/admin/Dropbox (Technion Dropbox)/PROJECTS/andrewL/pydock/IQ-
> motif-M1/project13584_2077.pdb"
Summary of feedback from opening /Users/admin/Dropbox (Technion
Dropbox)/PROJECTS/andrewL/pydock/IQ-motif-M1/project13584_2077.pdb
---
warnings | Duplicate atom serial number found: 150
Duplicate atom serial number found: 151
Duplicate atom serial number found: 153
Duplicate atom serial number found: 155
Duplicate atom serial number found: 158
413 messages similar to the above omitted
Chain information for project13584_2077.pdb #12
---
Chain | Description
A | No description available
X | No description available
> display /a:28-30
> open "/Users/admin/Dropbox (Technion Dropbox)/PROJECTS/andrewL/pydock/IQ-
> motif-M1/project13584_2384.pdb"
Summary of feedback from opening /Users/admin/Dropbox (Technion
Dropbox)/PROJECTS/andrewL/pydock/IQ-motif-M1/project13584_2384.pdb
---
warnings | Duplicate atom serial number found: 150
Duplicate atom serial number found: 151
Duplicate atom serial number found: 153
Duplicate atom serial number found: 155
Duplicate atom serial number found: 158
413 messages similar to the above omitted
Chain information for project13584_2384.pdb #13
---
Chain | Description
A | No description available
X | No description available
> open "/Users/admin/Dropbox (Technion Dropbox)/PROJECTS/andrewL/pydock/IQ-
> motif-M1/project13584_3905.pdb"
Summary of feedback from opening /Users/admin/Dropbox (Technion
Dropbox)/PROJECTS/andrewL/pydock/IQ-motif-M1/project13584_3905.pdb
---
warnings | Duplicate atom serial number found: 150
Duplicate atom serial number found: 151
Duplicate atom serial number found: 153
Duplicate atom serial number found: 155
Duplicate atom serial number found: 158
413 messages similar to the above omitted
Chain information for project13584_3905.pdb #14
---
Chain | Description
A | No description available
X | No description available
> hide #13 models
> hide #12 models
> hide #11 models
> display /a:28-30
> open "/Users/admin/Dropbox (Technion Dropbox)/PROJECTS/andrewL/pydock/IQ-
> motif-M4/project13585_207.pdb"
Summary of feedback from opening /Users/admin/Dropbox (Technion
Dropbox)/PROJECTS/andrewL/pydock/IQ-motif-M4/project13585_207.pdb
---
warnings | Duplicate atom serial number found: 150
Duplicate atom serial number found: 151
Duplicate atom serial number found: 153
Duplicate atom serial number found: 155
Duplicate atom serial number found: 158
413 messages similar to the above omitted
Chain information for project13585_207.pdb #15
---
Chain | Description
A | No description available
X | No description available
> open "/Users/admin/Dropbox (Technion Dropbox)/PROJECTS/andrewL/pydock/IQ-
> motif-M4/project13585_2810.pdb"
Summary of feedback from opening /Users/admin/Dropbox (Technion
Dropbox)/PROJECTS/andrewL/pydock/IQ-motif-M4/project13585_2810.pdb
---
warnings | Duplicate atom serial number found: 150
Duplicate atom serial number found: 151
Duplicate atom serial number found: 153
Duplicate atom serial number found: 155
Duplicate atom serial number found: 158
413 messages similar to the above omitted
Chain information for project13585_2810.pdb #16
---
Chain | Description
A | No description available
X | No description available
> display /a:28-30
> open "/Users/admin/Dropbox (Technion Dropbox)/PROJECTS/andrewL/pydock/IQ-
> motif-M4/project13585_7227.pdb"
Summary of feedback from opening /Users/admin/Dropbox (Technion
Dropbox)/PROJECTS/andrewL/pydock/IQ-motif-M4/project13585_7227.pdb
---
warnings | Duplicate atom serial number found: 150
Duplicate atom serial number found: 151
Duplicate atom serial number found: 153
Duplicate atom serial number found: 155
Duplicate atom serial number found: 158
413 messages similar to the above omitted
Chain information for project13585_7227.pdb #17
---
Chain | Description
A | No description available
X | No description available
> display /a:28-30
> display /a:28-30
> hide #14 models
> hide #15 models
> hide #16 models
> open "/Users/admin/Dropbox (Technion Dropbox)/PROJECTS/andrewL/pydock/IQ-
> motif-M4/project13585_9846.pdb"
Summary of feedback from opening /Users/admin/Dropbox (Technion
Dropbox)/PROJECTS/andrewL/pydock/IQ-motif-M4/project13585_9846.pdb
---
warnings | Duplicate atom serial number found: 150
Duplicate atom serial number found: 151
Duplicate atom serial number found: 153
Duplicate atom serial number found: 155
Duplicate atom serial number found: 158
413 messages similar to the above omitted
Chain information for project13585_9846.pdb #18
---
Chain | Description
A | No description available
X | No description available
> display /a:28-30
> open "/Users/admin/Dropbox (Technion Dropbox)/PROJECTS/andrewL/pydock/IQ-
> motif-M4/project13585_3903.pdb"
Summary of feedback from opening /Users/admin/Dropbox (Technion
Dropbox)/PROJECTS/andrewL/pydock/IQ-motif-M4/project13585_3903.pdb
---
warnings | Duplicate atom serial number found: 150
Duplicate atom serial number found: 151
Duplicate atom serial number found: 153
Duplicate atom serial number found: 155
Duplicate atom serial number found: 158
413 messages similar to the above omitted
Chain information for project13585_3903.pdb #19
---
Chain | Description
A | No description available
X | No description available
> close session
> open "/Users/admin/Dropbox (Technion Dropbox)/PROJECTS/andrewL/pydock/IQ-
> motif-M1/project13584_lig.nip.pdb" "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/andrewL/pydock/IQ-motif-M1/project13584_rec.nip.pdb"
Chain information for project13584_lig.nip.pdb #1
---
Chain | Description
A | No description available
Chain information for project13584_rec.nip.pdb #2
---
Chain | Description
X | No description available
> color @@bfactor > 0.4 red
> color @@bfactor > 0.2 red
> color @@bfactor > 0.2 gold
> color @@bfactor > 0.3 orange
> color @@bfactor > 0.4 red
> display
> rainbow chains
> color @@bfactor > 0.2 gold
> color @@bfactor > 0.3 orange
> color @@bfactor > 0.4 red
> ~display
> color #1 grey
> color 21 grey
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #2 grey
> color #1 light green
> hide #2 models
> show #2 models
> color @@bfactor > 0.2 gold
> color @@bfactor > 0.3 orange
> color @@bfactor > 0.4 red
> display /a:28-30
> show /x:102-104
> color ~C byatom
> style sphere
Changed 3360 atom styles
> save "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/andrewL/chimerax/NIPS_IQ-M1.cxs"
> color #2 light grey
> color #2 tan
> color ~C byatom
> color @@bfactor > 0.2 gold
> color @@bfactor > 0.3 orange
> color @@bfactor > 0.4 red
> display @@bfactor > 0.2
> color /x:102-104 green
> color /a:28-30 green
> color @@bfactor > 0.2 gold
> color @@bfactor > 0.3 orange
> color @@bfactor > 0.4 red
> save "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/andrewL/chimerax/NIPS_IQ-M1.cxs"
opened ChimeraX session
> turn x 10 models #1
> turn y 10 models #1
> turn x 10 models #1
> turn x 10 models #1
> turn x 10 models #1
> turn x 10 models #1
> turn x 10 models #1
> turn x 10 models #1
> turn x 10 models #1
> turn x 10 models #1
> turn x 10 models #1
> turn x 10 models #1
> turn x 10 models #1
> turn x 10 models #1
> turn x 10 models #1
> turn x 10 models #1
> turn x 10 models #1
> turn x 10 models #1
> turn y 10 models #1
> turn z 10 models #1
> turn z 10 models #1
> turn z 10 models #1
> turn z 10 models #1
> turn z 10 models #1
> turn z 10 models #1
> turn z 10 models #1
> turn z 10 models #1
> turn z 10 models #1
> turn z 10 models #1
> turn z 10 models #1
> turn z 10 models #1
> turn z 10 models #1
> turn z 10 models #1
> turn z 10 models #1
> turn z 10 models #1
> turn z 10 models #1
> turn z 10 models #1
> turn z 10 models #1
> turn z 10 models #1
> turn z 10 models #1
> turn z 10 models #1
> turn z 10 models #1
> turn z 10 models #1
> turn z 10 models #1
> turn z 10 models #1
> move x 10 models #1
> move x 10 models #1
> move x 10 models #1
> move x 10 models #1
> move x 10 models #1
> move x 10 models #1
> move x 10 models #1
> move x 10 models #1
> move x 10 models #1
> color /a:28-30 /x:102-104 violet
> color @@bfactor > 0.2 green
> save "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/andrewL/chimerax/NIP.M1.f1.jpg" width 1963 height 1218
> supersample 3
> save "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/andrewL/chimerax/NIPS_IQ-M1.cxs"
> turn y -180 models #1 center #1
> turn y -180 models #1 center #1
> turn y -180 models #1 center #1
> turn y -180 models #2 center #2
> save "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/andrewL/chimerax/NIPS_IQ-M1.f2.cxs"
opened ChimeraX session
> display
> color light green
> ~ribbon
> color @@bfactor < -5 green
> color @@bfactor > 0 green
> color grey
> color light grey
> color grey
> color @@bfactor > 0.2 light grey green
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color @@bfactor > 0.2 light green
> color @@bfactor > 0.3 green
> color /a:28-30 /x:102-104 violet
> turn x 5 models #1
> turn x -5 models #1
> turn x -5 models #1
> turn x -5 models #1
> turn x -5 models #1
> turn x -5 models #1
> turn x -5 models #1
> turn x -5 models #1
> turn x -5 models #1
> turn x -5 models #2
> turn y -5 models #2
> turn y -5 models #2
> turn y -5 models #2
> turn y -5 models #2
> turn y -5 models #2
> turn y -5 models #2
> turn y -5 models #2
> turn y -5 models #2
> turn y -5 models #2
> turn y -5 models #2
> turn y -5 models #2
> turn y -5 models #2
> turn y -5 models #2
> turn y -5 models #2
> turn y -5 models #2
> turn y -5 models #2
> turn y -5 models #2
> turn y -5 models #2
> turn y -5 models #2
> turn y -5 models #2
> turn y -5 models #2
> turn y -5 models #2
> turn y -5 models #2
> turn y -5 models #2
> turn y -5 models #2
> turn y -5 models #2
> turn y -5 models #2
> turn y -5 models #2
> turn y -5 models #2
> turn y -5 models #2
> turn y -5 models #2
> turn y -5 models #2
> turn y -5 models #2
> turn y -5 models #2
> turn y -5 models #1
> turn y -5 models #1
> turn y -5 models #1
> turn y -5 models #1
> turn y -5 models #1
> turn y -5 models #1
> turn y -5 models #1
> turn y -5 models #1
> turn y -5 models #1
> turn y -5 models #1
> turn x -5 models #1
> turn x -5 models #1
> turn x -5 models #1
> turn x -5 models #1
> turn x -5 models #1
> turn x -5 models #1
> turn x -5 models #1
> lighting shadows true
> lighting flat
> lighting full
> graphics silhouettes false
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting simple
> lighting shadows true
> graphics silhouettes true
> graphics silhouettes false
> lighting flat
> lighting full
> lighting soft
> graphics silhouettes false
> lighting shadows true intensity 0.5
> graphics silhouettes true
> graphics silhouettes false
> color @@bfactor > 0.2 light green
> color @@bfactor > 0.4 green
> save "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/andrewL/chimerax/NIPS_IQ-M1.cxs"
opened ChimeraX session
> turn y -5 models #2
> turn y -5 models #2
> turn y -5 models #2
> turn y -5 models #2
> turn y -5 models #2
> turn y -5 models #2
> turn y -5 models #2
> turn y -5 models #2
> turn y -5 models #2
> ~display
> ribbon
> alias mut sel /a:28-30 /x:102-104
> display mut
> show mut
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> display sel
> mut
48 atoms, 46 bonds, 2 models selected
> display sel
> rep stick
Unknown command: rep stick
> rep stick
Unknown command: rep stick
> style stick
Changed 3360 atom styles
> select clear
> color ~C byatom
> style sphere
Changed 3360 atom styles
> lighting shadows false
> lighting flat
> lighting flat
> lighting full
> graphics silhouettes false
> lighting soft
> lighting simple
> lighting soft
> lighting full
> graphics silhouettes true
> graphics silhouettes false
> lighting soft
> lighting full
> lighting flat
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting simple
> graphics silhouettes true
> graphics silhouettes false
> save "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/andrewL/chimerax/NIPS_IQ-M1.cxs"
opened ChimeraX session
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #2 center #2
> turn y 5 models #2 center #2
> turn y 5 models #2 center #2
> turn y 5 models #2 center #2
> turn y 5 models #2 center #2
> turn y 5 models #2 center #2
> turn y 5 models #2 center #2
> turn y 5 models #2 center #2
> turn y 5 models #2 center #2
> turn y 5 models #2 center #2
> turn y 5 models #2 center #2
> turn y 5 models #2 center #2
> turn y 5 models #2 center #2
> turn y 5 models #2 center #2
> turn y 5 models #2 center #2
> turn y 5 models #2 center #2
> turn y 5 models #2 center #2
> turn y 5 models #2 center #2
> turn y 5 models #2 center #2
> save "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/andrewL/chimerax/NIPS_IQ-M1.f2.cxs"
> display
> color grey
> color @@bfactor > 0.2 light green
> color @@bfactor > 0.4 green
> color /a:28-30 /x:102-104 violet
> color @@bfactor > 0.2 light green
> color @@bfactor > 0.4 green
> color C & /a:28-30 /x:102-104 violet
> color ~C & /a:28-30 /x:102-104 byatom
> color @@bfactor > 0.2 light green
> color @@bfactor > 0.4 green
> color ~C & /a:28-30 /x:102-104 byatom
> save "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/andrewL/chimerax/NIPS_IQ-M1.f3.cxs"
> ~ribbon
> save "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/andrewL/chimerax/NIPS_IQ-M1.f3.cxs"
> turn y -5 models #2 center #2
> turn y -5 models #2 center #2
> turn y -5 models #2 center #2
> turn y -5 models #2 center #2
> turn y -5 models #2 center #2
> turn y -5 models #2 center #2
> turn y -5 models #2 center #2
> turn y -5 models #2 center #2
> turn y -5 models #2 center #2
> turn y -5 models #2 center #2
> turn y -5 models #2 center #2
> turn y -5 models #2 center #2
> turn y -5 models #2 center #2
> turn y -5 models #2 center #2
> turn y -5 models #2 center #2
> turn y -5 models #2 center #2
> turn y -5 models #2 center #2
> ~display
> ribbon
> display @@bfactor > 0.2
> display /a:28-30 /x:102-104
> turn y -5 models #1 center #1
> turn y -5 models #1 center #1
> turn y -5 models #1 center #1
> turn y -5 models #1 center #1
> turn y -5 models #1 center #1
> turn y -5 models #1 center #1
> turn y -5 models #1 center #1
> turn y -5 models #1 center #1
> turn y -5 models #1 center #1
> turn y -5 models #1 center #1
> turn y -5 models #1 center #1
> turn y -5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y 5 models #1 center #1
> turn y -5 models #1 center #1
> turn y -5 models #1 center #1
> turn y -5 models #1 center #1
> turn y -5 models #1 center #1
> turn y -5 models #1 center #1
> turn y -5 models #1 center #1
> turn y -5 models #1 center #1
> turn y -5 models #1 center #1
> turn y -5 models #1 center #1
> turn y -5 models #1 center #1
> turn y -5 models #1 center #1
> turn y -5 models #1 center #1
> turn y -5 models #1 center #1
> turn y -5 models #1 center #1
> turn y -5 models #1 center #1
> turn y -5 models #1 center #1
> turn y -5 models #1 center #1
> turn y -5 models #1 center #1
> turn y -5 models #1 center #1
> save "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/andrewL/chimerax/NIPS_IQ-M1.f1.cxs"
> ~ribbon
Drag select of 259 atoms
> display
> ~ribbon
> style stick
Changed 3360 atom styles
> style sel sphere
Changed 259 atom styles
> style sphere
Changed 3360 atom styles
> transparency 90
> transparency 90 target a
> transparency sel 0 target a
> select up
1034 atoms, 1048 bonds, 2 models selected
> select up
3360 atoms, 3416 bonds, 2 models selected
> select up
3360 atoms, 3416 bonds, 2 models selected
> select up
3360 atoms, 3416 bonds, 2 models selected
> select up
3360 atoms, 3416 bonds, 2 models selected
> transparency 80 target a
> transparency 50 target a
> transparency sel 0 target a
> ~display
> display sel
> select clear
> select @@bfactor > 0.2
222 atoms, 213 bonds, 2 models selected
> ~display
> display @@bfactor > 0.2 | /a:28-30 /x:102-104
> select clear
> select @@bfactor > 0.2 | /a:28-30 /x:102-104
259 atoms, 249 bonds, 2 models selected
> transparency ~sel 50 target a
> display
> ~ribbon
> transparency ~sel 60 target a
> transparency ~sel 70 target a
> color /a:28-30 /x:102-104 violet
> color ~C & /a:28-30 /x:102-104 byatom
> ribbon
> transparency 70 target r
> select clear
> select @@bfactor > 0.2 | /a:28-30 /x:102-104
259 atoms, 249 bonds, 2 models selected
> transparency ~sel 90 target a
> transparency ~sel 80 target a
> transparency ~sel 85 target a
> ~ribbon
> select clear
> ~display backbone
> display
> ribbon
> save "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/andrewL/chimerax/NIPS_IQ-M1.f4.cxs"
> transparency 85 target r
> transparency 5 target r
> transparency 0 target r
> transparency 10 target r
> transparency 2 target r
> transparency 0 target r
> color white target r
> ~display
> color grey target r
> display @@bfactor > 0.2 | /a:28-30 /x:102-104
> color light grey target r
> color grey target r
> transparency 50 target r
> transparency 80 target r
> transparency 70 target r
> transparency 50 target r
> lighting shadows true
> lighting flat
> lighting full
> lighting soft
> lighting simple
> graphics silhouettes false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> save "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/andrewL/chimerax/NIPS_IQ-M1.cxs"
> lighting shadows false
> lighting full
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting shadows false
> lighting flat
> lighting full
> graphics silhouettes false
> display
> transparency 0
> transparency 0 target a
> style stick
Changed 3360 atom styles
> lighting full
> lighting soft
> lighting simple
> style sphere
Changed 3360 atom styles
> select @@bfactor > 0.2 | /a:28-30 /x:102-104
259 atoms, 249 bonds, 2 models selected
> color ~sel light grey
> select clear
> ~ribbon
> lighting simple
> lighting soft
> lighting full
> ui tool show "Side View"
> lighting shadows false
> ~siap
Unknown command: ~siap
> ~siap
Unknown command: ~siap
> ~display
> display @@bfactor > 0.2 | /a:28-30 /x:102-104 :< 4
> ribbon
> lighting shadows true
> lighting flat
> lighting shadows true intensity 0.5
> lighting simple
> lighting soft
> lighting shadows true intensity 0.5
> lighting simple
> lighting shadows true
> graphics silhouettes false
> color ~C byatom
> style stick
Changed 3360 atom styles
> color @@bfactor > 0.2 light green
> color @@bfactor > 0.3 green
> style sphere
Changed 3360 atom styles
> color light grey
> color tan
> color @@bfactor > 0.2 light green
> color @@bfactor > 0.3 green
> color @@bfactor > 0.2 light green
> color @@bfactor > 0.4 green
> volume /a:28-30 /x:102-104 violet
Expected a keyword
> color /a:28-30 /x:102-104 violet
> ~display
> display @@bfactor > 0.2 | /a:28-30 /x:102-104
> display /x:104 < 4
> show /x:104 < 4
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> display /x:104 :< 4
> style /x:104 :< 4 stick
Changed 118 atom styles
> style @@bfactor > 0.2 | /a:28-30 /x:102-104 sphere
Changed 259 atom styles
> color /x:104 :< 4 byatom
> color C tan
> color /a:28-30 /x:102-104 violet
> color @@bfactor > 0.2 light green
> color @@bfactor > 0.4 green
> ~display :106,107
> ~display :106,107,100
> save "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/andrewL/chimerax/NIPS_IQ-M1.cxs"
> style sphere
Changed 3360 atom styles
> lighting shadows false
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting flat
> lighting full
> graphics silhouettes false
> lighting shadows false
> ~display :106,107,100,108
> save "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/andrewL/chimerax/NIP.M1.f8.jpg" width 1963 height 1218
> supersample 3
> save "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/andrewL/chimerax/NIP.M1.f9.jpg" width 1963 height 1218
> supersample 3
> ~display :106,107,100,108,99
> ~display :106,107,100,108,99,101
> style stick
Changed 3360 atom styles
> color ~C byatom
> transparency 100 target r
> transparency 90 target r
> transparency 0 target r
> cartoon style width 1.5 thickness 0.3
> cartoon style width 1.5 thickness 0.2
> cartoon style width 1.5 thickness 0.3
> cartoon style width 1 thickness 0.3
> cartoon style width 1.2 thickness 0.3
> cartoon style width 1.2 thickness 0.25
> transparency 50 target r
> label
> label
> label
> label tar a
Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword
> label residues
> ~ribbon
Drag select of 203 atoms, 199 bonds
> label sel
> select clear
> ribbon
> style sphere
Changed 3360 atom styles
> size #1:138 #2:176 stickRadius 0.3
Changed 7 bond radii
> style stick
Changed 3360 atom styles
> select up
Nothing selected
> select up
Nothing selected
> select up
Nothing selected
> select up
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> select up
Nothing selected
> style sphere
Changed 3360 atom styles
> size stickRadius 0.3
Changed 3416 bond radii
> style stick
Changed 3360 atom styles
> select up
Nothing selected
> ~display :105
> style sphere
Changed 3360 atom styles
> save "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/andrewL/chimerax/NIP.M1.f10.jpg" width 1963 height 1218
> supersample 3
> save "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/andrewL/chimerax/NIP.M1.f11.jpg" width 1963 height 1218
> supersample 3
> style stick
Changed 3360 atom styles
> save "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/andrewL/chimerax/NIP.M1.f12.jpg" width 1963 height 1218
> supersample 3
> save "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/andrewL/chimerax/NIPS_IQ-M1.cxs"
opened ChimeraX session
> open 5NLY
5nly title:
Brag2 Sec7-PH (390-763), P212121 [more info...]
Chain information for 5nly #3
---
Chain | Description
A B | IQ motif and SEC7 domain-containing protein 1
Non-standard residues in 5nly #3
---
PO4 — phosphate ion
5nly mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> mmaker #3 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker project13584_lig.nip.pdb, chain A (#1) with 5nly, chain B (#3),
sequence alignment score = 57.3
RMSD between 7 pruned atom pairs is 1.487 angstroms; (across all 52 pairs:
12.312)
> mmaker #3 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker project13584_rec.nip.pdb, chain X (#2) with 5nly, chain A (#3),
sequence alignment score = 1571.1
RMSD between 341 pruned atom pairs is 0.675 angstroms; (across all 345 pairs:
0.713)
> rainbow #3 chains
> report
Unknown command: report
> help
OpenGL version: 4.1 ATI-3.9.15
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac18,3
Processor Name: Quad-Core Intel Core i7
Processor Speed: 4.2 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 8 MB
Hyper-Threading Technology: Enabled
Memory: 64 GB
Boot ROM Version: 183.0.0.0.0
SMC Version (system): 2.41f2
Software:
System Software Overview:
System Version: macOS 10.15.5 (19F101)
Kernel Version: Darwin 19.5.0
Time since boot: 20 days 1:17
Graphics/Displays:
Radeon Pro 580:
Chipset Model: Radeon Pro 580
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 8 GB
Vendor: AMD (0x1002)
Device ID: 0x67df
Revision ID: 0x00c0
ROM Revision: 113-D000AA-931
VBIOS Version: 113-D0001A1X-025
EFI Driver Version: 01.00.931
Metal: Supported, feature set macOS GPUFamily2 v1
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: 5120 x 2880 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8
File attachment: generate.V1.py
Attachments (1)
Change History (8)
by , 5 years ago
| Attachment: | generate.V1.py added |
|---|
comment:1 by , 5 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Graphics |
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → --offscreen does not work on Mac (or Windows) |
Reported by Fabian Glaser
comment:2 by , 5 years ago
| Summary: | --offscreen does not work on Mac (or Windows) → --offscreen does not work on Linux (or Mac, or Windows) |
|---|
comment:3 by , 5 years ago
I tried ChimeraX 1.0 offscreen rendering on ubuntu 18.04
chimerax --offscreen --nogui test.cxc
where test.cxc contains "open 1a0m ; save test.png" and it worked correctly loading the PDB model and saving an image. The reported error has PyOpenGL platform _p = None in PyOpenGL code suggests that the reporters linux failed when asked to use OSMesa in chimerax/graphics/opengl.py
from OpenGL.platform import PLATFORM as _p
from OpenGL.error import _ErrorChecker
if _ErrorChecker:
_error_checker = _ErrorChecker( _p, _p.GL.glGetError )
else:
_error_checker = None
comment:4 by , 5 years ago
Offscreen rendering is only supported on Linux. Since it fails on your Linux system you should report the error from your Linux ChimeraX so we know details of your operating system and ChimeraX version.
comment:5 by , 5 years ago
Dear Tom, Greg,
Thanks for your help. Here is the failure when the script is launched on the Linux system, below that is the usage with only the —nogui, so you can see that the script runs ok.
1. with —nogui —offscreen
/home/avivr/chimerax/chimerax_1.0/usr/bin/chimerax --script "generate.V5.py inp1.txt" --nogui --offscreen
Traceback (most recent call last):
File "/home/avivr/chimerax/chimerax_1.0/usr/lib/ucsf-chimerax/lib/python3.7/runpy.py", line 193, in _run_module_as_main
"__main__", mod_spec)
File "/home/avivr/chimerax/chimerax_1.0/usr/lib/ucsf-chimerax/lib/python3.7/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/home/avivr/chimerax/chimerax_1.0/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/ChimeraX_main.py", line 895, in <module>
exit_code = init(sys.argv)
File "/home/avivr/chimerax/chimerax_1.0/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/ChimeraX_main.py", line 453, in init
sess = session.Session(app_name, debug=opts.debug, silent=opts.silent)
File "/home/avivr/chimerax/chimerax_1.0/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/core/session.py", line 441, in __init__
self.logger = logger.Logger(self)
File "/home/avivr/chimerax/chimerax_1.0/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/core/session.py", line 501, in __setattr__
if not name.startswith('_') and self.snapshot_methods(value, base_type=StateManager) is not None:
File "/home/avivr/chimerax/chimerax_1.0/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/core/session.py", line 535, in snapshot_methods
from chimerax import graphics as gr
File "/home/avivr/chimerax/chimerax_1.0/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/graphics/__init__.py", line 34, in <module>
from .opengl import Texture, Lighting, Material
File "/home/avivr/chimerax/chimerax_1.0/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/graphics/opengl.py", line 61, in <module>
from OpenGL import GL
File "/home/avivr/chimerax/chimerax_1.0/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/PyOpenGL-3.1.5-py3.7.egg/OpenGL/GL/__init__.py", line 4, in <module>
from OpenGL.GL.VERSION.GL_1_1 import *
File "/home/avivr/chimerax/chimerax_1.0/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/PyOpenGL-3.1.5-py3.7.egg/OpenGL/GL/VERSION/GL_1_1.py", line 14, in <module>
from OpenGL.raw.GL.VERSION.GL_1_1 import *
File "/home/avivr/chimerax/chimerax_1.0/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/PyOpenGL-3.1.5-py3.7.egg/OpenGL/raw/GL/VERSION/GL_1_1.py", line 7, in <module>
from OpenGL.raw.GL import _errors
File "/home/avivr/chimerax/chimerax_1.0/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/PyOpenGL-3.1.5-py3.7.egg/OpenGL/raw/GL/_errors.py", line 4, in <module>
_error_checker = _ErrorChecker( _p, _p.GL.glGetError )
AttributeError: 'NoneType' object has no attribute 'glGetError'
2. only —nogui
/home/avivr/chimerax/chimerax_1.0/usr/bin/chimerax --script "generate.V5.py inp1.txt" --nogui
0.00% done: Initializing core
50.00% done: Initializing bundles
Executing: runscript generate.V5.py inp1.txt
{'PDB1': '1WMB', 'PDB2': '3I3O', 'CHAIN1': 'A', 'CHAIN2': 'A', 'RES1': '138', 'RES2': '176', 'COD1': 'xxx', 'COD2': 'yyy'}
Executing: close
Executing: graphics bgColor white
Executing: open 1WMB
Fetching mmCIF 1wmb, 0.108 of 0.108 Mbytes received
Opening mmCIF 1wmb
Fetching CCD MG, 0.00331 of 0.00331 Mbytes received
Fetching CCD CAC, 0.00459 of 0.00459 Mbytes received
Summary of feedback from opening 1WMB fetched from pdb
---
_notes_ | Fetching compressed mmCIF 1wmb from
http://files.rcsb.org/download/1wmb.cif
Fetching CCD MG from http://ligand-expo.rcsb.org/reports/M/MG/MG.cif
Fetching CCD CAC from http://ligand-expo.rcsb.org/reports/C/CAC/CAC.cif
_1wmb_ title:
**Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase**
[[more info...]](cxcmd:log metadata #1)
Chain information for 1wmb #1
---
Chain | Description
[A](cxcmd:select /A:1-260 "Select chain") [B](cxcmd:select /B:1-260 "Select
chain") | [D(-)-3-hydroxybutyrate dehydrogenase](cxcmd:sequence chain #1/A#1/B
"Show sequence")
Non-standard residues in 1wmb #1
---
[CAC](cxcmd:sel :CAC "select residue") — [cacodylate
ion](http://www.rcsb.org/ligand/CAC "show residue info") (dimethylarsinate)
[MG](cxcmd:sel :MG "select residue") — [magnesium
ion](http://www.rcsb.org/ligand/MG "show residue info")
1wmb mmCIF Assemblies | [1](cxcmd:sym #1 assembly 1 ; view "Generate
assembly")| author_and_software_defined_assembly
Executing: open 3I3O
Fetching mmCIF 3i3o, 0.449 of 0.449 Mbytes received
Opening mmCIF 3i3o
Fetching CCD NAE, 0.0131 of 0.0131 Mbytes received
Fetching CCD CL, 0.00329 of 0.00329 Mbytes received
Summary of feedback from opening 3I3O fetched from pdb
---
_notes_ | Fetching compressed mmCIF 3i3o from
http://files.rcsb.org/download/3i3o.cif
Fetching CCD NAE from http://ligand-expo.rcsb.org/reports/N/NAE/NAE.cif
Fetching CCD CL from http://ligand-expo.rcsb.org/reports/C/CL/CL.cif
_3i3o_ title:
**2.06 Angstrom resolution crystal structure of a short chain dehydrogenase
from Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone**
[[more info...]](cxcmd:log metadata #2)
Chain information for 3i3o #2
---
Chain | Description
[A](cxcmd:select #2/A:7-288 "Select chain") [B](cxcmd:select #2/B:6-288
"Select chain") [C](cxcmd:select #2/C:8-288 "Select chain") [D](cxcmd:select
#2/D:6-288 "Select chain") [E](cxcmd:select #2/E:10-288 "Select chain")
[F](cxcmd:select #2/F:19-288 "Select chain") [G](cxcmd:select #2/G:27-288
"Select chain") [H](cxcmd:select #2/H:14-288 "Select chain") | [Short chain
dehydrogenase](cxcmd:sequence chain #2/A#2/B#2/C#2/D#2/E#2/F#2/G#2/H "Show
sequence")
Non-standard residues in 3i3o #2
---
[CAC](cxcmd:sel :CAC "select residue") — [cacodylate
ion](http://www.rcsb.org/ligand/CAC "show residue info") (dimethylarsinate)
[CL](cxcmd:sel :CL "select residue") — [chloride
ion](http://www.rcsb.org/ligand/CL "show residue info")
[MG](cxcmd:sel :MG "select residue") — [magnesium
ion](http://www.rcsb.org/ligand/MG "show residue info")
[NAE](cxcmd:sel :NAE "select residue") — [nicotinamide adenine dinucleotide
acetone adduct](http://www.rcsb.org/ligand/NAE "show residue info")
3i3o mmCIF Assemblies | [1](cxcmd:sym #2 assembly 1 ; view "Generate
assembly")| author_and_software_defined_assembly | [2](cxcmd:sym #2 assembly 2
; view "Generate assembly")| author_and_software_defined_assembly
Executing: delete #1 & ~/A
Executing: delete #2 & ~/A
Executing: delete ~protein
Executing: ~display
Executing: ribbon
Executing: mmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment score = 499.7
Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment score = 499.7
RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: 3.736)
RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: 3.736)
Executing: color #1 green
Colored 1879 atoms, 0 surfaces, 260 residues, rings, and 1905 bonds
Executing: color #2 tan
Colored 2160 atoms, 0 surfaces, 282 residues, rings, and 2202 bonds
Executing: color ~C byatom
Colored 1491 atoms, 0 surfaces, 542 residues, and rings
Executing: 2dlabels text "1WMB A:138" color green size 40 xpos .03 ypos .90
Executing: 2dlabels text "3I3O A:176" color tan size 40 xpos .03 ypos .82
Executing: alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2
Executing: alias sel-3 sel #1:137-139 #2:175-177
Executing: sel-ca
13 atoms, 1 model selected
13 atoms, 1 model selected
26 atoms, 2 models selected
26 atoms, 2 models selected
Executing: surface sel-residues enclose sel-residues
Executing: transparency 0 ribbons
Set transparency of 542 residues
Executing: ~select
Nothing selected
Nothing selected
Executing: save fig1.jpg
Unable to save images because OpenGL rendering is not available
Best,
Fabian
Fabian Glaser PhD
Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa, Israel
Web https://lokey.technion.ac.il/bioinformatic-knowledge-unit/
Tel +972 (0) 4 8293701
On 4 Aug 2020, at 3:19, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu<mailto:ChimeraX-bugs-admin@cgl.ucsf.edu>> wrote:
#3582: --offscreen does not work on Linux (or Mac, or Windows)
--------------------------------+------------------------
Reporter: fglaser@… | Owner: Greg Couch
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Graphics | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
--------------------------------+------------------------
Comment (by Tom Goddard):
Offscreen rendering is only supported on Linux. Since it fails on your
Linux system you should report the error from your Linux ChimeraX so we
know details of your operating system and ChimeraX version.
--
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follow-up: 5 comment:6 by , 5 years ago
We need to know about your Linux OS and which ChimeraX you have installed, since --offscreen is working on Ubuntu 18.04 with ChimeraX 1.0 so we believe the problem is some incompatibility with your Linux. Could you start ChimeraX on the Linux machine in gui mode and use Help / Report Bug... and in the description say "This is the machine where --offscreen does not work described in bug #3582."
follow-up: 6 comment:7 by , 5 years ago
| Resolution: | → worksforme |
|---|---|
| Status: | assigned → closed |
Need more information about Linux system to help figure out where the bug is.
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