![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 years ago
Closed 4 years ago
#6183 closed defect (can't reproduce)
Sequence viewer not tracked by alignments manager
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sequence | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /System/Volumes/Data/scicore/projects/scicore-p-maiert-
> structbio/delbartf/ACC/cryo-
> EM/Timm_reprocess/ChimeraX/ACC_Cit_localresmap.cxs
Opened cryosparc_P6_J773_005_volume_map.mrc as #1, grid size 480,480,480,
pixel 1.06, shown at level 0.147, step 1, values float32
Opened cryosparc_P6_J775_map_locres.mrc as #2, grid size 480,480,480, pixel
1.06, shown at level 0.000418, step 1, values float32
Map values for surface "surface": minimum 0, mean 3.557, maximum 7.328
Log from Tue Feb 15 19:16:03 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /System/Volumes/Data/scicore/projects/scicore-p-maiert-
> structbio/delbartf/ACC/cryo-
> EM/Timm_reprocess/ChimeraX/ACC_figures_test_session.cxs format session
Opened cryosparc_P6_J773_005_volume_map_sharp.mrc as #2, grid size
480,480,480, pixel 1.06, shown at level 0.177, step 1, values float32
Log from Fri Feb 11 17:52:40 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /System/Volumes/Data/scicore/projects/scicore-p-maiert-
> structbio/delbartf/ACC/4_dimers.cxs
Opened cryosparc_P6_J572_008_volume_map_sharp.mrc as #2, grid size
480,480,480, pixel 1.06, shown at level 0.151, step 1, values float32
opened ChimeraX session
> molmap #3 5
Opened hACC_complete_4_dimers.pdb map 5 as #4, grid size 140,124,386, pixel
1.67, shown at level 0.102, step 1, values float32
> hide #!3 models
> select #3
127120 atoms, 129736 bonds, 336 pseudobonds, 16168 residues, 2 models selected
> ~select #3
8 models selected
> save /System/Volumes/Data/scicore/projects/scicore-p-maiert-
> structbio/delbartf/ACC/cryo-EM/Filament_tracer/hACC_4dimers_molmap_5A.mrc
> models #4
> open 6g2d
6g2d title:
Citrate-induced acetyl-CoA carboxylase (ACC-Cit) filament at 5.4 A resolution
[more info...]
Chain information for 6g2d #5
---
Chain | Description | UniProt
B C D F | Acetyl-CoA carboxylase 1 | ACACA_HUMAN
> hide #!4 models
> select #5
88169 atoms, 89088 bonds, 25 pseudobonds, 5501 residues, 2 models selected
> ~select #5
Nothing selected
> molmap #5 5
Opened 6g2d map 5 as #6, grid size 100,130,188, pixel 1.67, shown at level
0.102, step 1, values float32
> ui mousemode right distance
> hide #!6 models
> select #5
88169 atoms, 89088 bonds, 25 pseudobonds, 5501 residues, 2 models selected
> ~select #5
Nothing selected
> distance #5/D:497@NE2 #5/C:2336@HG3
Distance between 6g2d #5/D HIS 497 NE2 and /C ARG 2336 HG3: 183.088Å
> distance #5/D:1091@HD2 #5/D:1368@HH22
Distance between 6g2d #5/D PRO 1091 HD2 and ARG 1368 HH22: 29.211Å
> distance #5/C:1111@OH #5/F:1440@OE1
Distance between 6g2d #5/C TYR 1111 OH and /F GLU 1440 OE1: 43.700Å
> distance #5/F:1440@CA #5/D:1047@N
Distance between 6g2d #5/F GLU 1440 CA and /D GLN 1047 N: 132.423Å
> close
> open /System/Volumes/Data/scicore/projects/scicore-p-maiert-
> structbio/delbartf/ACC/cryo-
> EM/Timm_reprocess/ChimeraX/ACC_figures_test_session.cxs format session
Unable to restore session, resetting.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 691, in restore
self.reset()
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 535, in reset
sm.reset_state(container, self)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/tools.py", line 292, in reset_state
tool_inst.delete()
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seq-view/tool.py", line 511, in delete
self.alignment.detach_viewer(self)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/alignment.py", line 398, in detach_viewer
self.session.alignments.destroy_alignment(self)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/manager.py", line 117, in destroy_alignment
del self._alignments[alignment.ident]
KeyError: '3'
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 691, in restore
self.reset()
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 535, in reset
sm.reset_state(container, self)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/tools.py", line 292, in reset_state
tool_inst.delete()
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seq-view/tool.py", line 511, in delete
self.alignment.detach_viewer(self)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/alignment.py", line 398, in detach_viewer
self.session.alignments.destroy_alignment(self)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/manager.py", line 117, in destroy_alignment
del self._alignments[alignment.ident]
KeyError: '3'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 333, in interceptRequest
self._callback(info)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 92, in _intercept
return interceptor(request_info, *args)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 366, in intercept
chimerax_intercept(*args, view=view, session=session)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 468, in chimerax_intercept
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 382, in thread_safe
func(*args, **kw)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 459, in defer
cxcmd(session, topic)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 477, in cxcmd
run(session, cmd)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 181, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 433, in collated_open
return remember_data_format()
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 403, in remember_data_format
models, status = func(*func_args, **func_kw)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 26, in open
return cxs_open(session, data, **kw)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 995, in open
session.restore(stream, path=path, resize_window=resize_window)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 733, in restore
self.reset()
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 535, in reset
sm.reset_state(container, self)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/tools.py", line 292, in reset_state
tool_inst.delete()
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seq-view/tool.py", line 511, in delete
self.alignment.detach_viewer(self)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/alignment.py", line 392, in detach_viewer
self.viewers.remove(viewer)
ValueError: list.remove(x): x not in list
ValueError: list.remove(x): x not in list
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/alignment.py", line 392, in detach_viewer
self.viewers.remove(viewer)
See log for complete Python traceback.
> open /System/Volumes/Data/scicore/projects/scicore-p-maiert-
> structbio/delbartf/ACC/cryo-
> EM/Timm_reprocess/ChimeraX/ACC_figures_test_session.cxs
Unable to restore session, resetting.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 691, in restore
self.reset()
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 535, in reset
sm.reset_state(container, self)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/tools.py", line 292, in reset_state
tool_inst.delete()
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seq-view/tool.py", line 511, in delete
self.alignment.detach_viewer(self)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/alignment.py", line 392, in detach_viewer
self.viewers.remove(viewer)
ValueError: list.remove(x): x not in list
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 691, in restore
self.reset()
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 535, in reset
sm.reset_state(container, self)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/tools.py", line 292, in reset_state
tool_inst.delete()
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seq-view/tool.py", line 511, in delete
self.alignment.detach_viewer(self)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/alignment.py", line 392, in detach_viewer
self.viewers.remove(viewer)
ValueError: list.remove(x): x not in list
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 267, in event
_open_dropped_file(self.session, event.file())
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 1919, in _open_dropped_file
run(session, 'open %s' % FileNameArg.unparse(path))
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 181, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 433, in collated_open
return remember_data_format()
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 403, in remember_data_format
models, status = func(*func_args, **func_kw)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 26, in open
return cxs_open(session, data, **kw)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 995, in open
session.restore(stream, path=path, resize_window=resize_window)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 733, in restore
self.reset()
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 535, in reset
sm.reset_state(container, self)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/tools.py", line 292, in reset_state
tool_inst.delete()
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seq-view/tool.py", line 511, in delete
self.alignment.detach_viewer(self)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/alignment.py", line 392, in detach_viewer
self.viewers.remove(viewer)
ValueError: list.remove(x): x not in list
ValueError: list.remove(x): x not in list
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/alignment.py", line 392, in detach_viewer
self.viewers.remove(viewer)
See log for complete Python traceback.
> set bgColor white
> lighting flat shadows false
> graphics silhouettes true
> open /Users/delbart/delbartf/ACC/cryo-
> EM/Timm_reprocess/ACC_NO_citrate_real_space_refined-ChainC-chainD-BUILD-Ala-
> mutated-res750.pdb
Chain information for ACC_NO_citrate_real_space_refined-ChainC-chainD-BUILD-
Ala-mutated-res750.pdb #1
---
Chain | Description
B | No description available
C | No description available
D | No description available
F | No description available
> open /Users/delbart/delbartf/ACC/cryo-
> EM/Timm_reprocess/cryosparc_P6_J773_005_volume_map_sharp.mrc
Opened cryosparc_P6_J773_005_volume_map_sharp.mrc as #2, grid size
480,480,480, pixel 1.06, shown at level 0.0807, step 2, values float32
> volume #2 style mesh level 0.177 step 1 color snow transparency 1
> select #1/C:1-621
7449 atoms, 7545 bonds, 521 residues, 1 model selected
> color sel firebrick
> select #1/C:622-747
1960 atoms, 1975 bonds, 126 residues, 1 model selected
> color sel chocolate
> select #1/C:748-846
1484 atoms, 1496 bonds, 99 residues, 1 model selected
> color sel magenta
> select #1/C:847-1092
4007 atoms, 4040 bonds, 246 residues, 1 model selected
> color sel orange
> select #1/C:1093-1161
1143 atoms, 1157 bonds, 69 residues, 1 model selected
> color sel yellow
> select #1/C:1162-1376
2117 atoms, 2138 bonds, 3 pseudobonds, 129 residues, 2 models selected
> color sel yellow green
> select #1/C:1377-1581
3244 atoms, 3274 bonds, 1 pseudobond, 199 residues, 2 models selected
> color sel forestgreen
> select #1/C:1581-2355
12078 atoms, 12219 bonds, 758 residues, 1 model selected
> color sel dodgerblue
> select #1/C:2339
Nothing selected
> color sel magenta
> select #1/D:1-621
7447 atoms, 7543 bonds, 520 residues, 1 model selected
> color sel firebrick
> select #1/D:622-747
1960 atoms, 1975 bonds, 126 residues, 1 model selected
> color sel chocolate
> select #1/D:748-846
1484 atoms, 1496 bonds, 99 residues, 1 model selected
> color sel magenta
> select #1/D:847-1092
4007 atoms, 4040 bonds, 246 residues, 1 model selected
> color sel orange
> select #1/D:1093-1161
1143 atoms, 1157 bonds, 69 residues, 1 model selected
> color sel yellow
> select #1/D:1162-1376
2117 atoms, 2138 bonds, 3 pseudobonds, 129 residues, 2 models selected
> color sel yellow green
> select #1/D:1377-1581
3244 atoms, 3274 bonds, 1 pseudobond, 199 residues, 2 models selected
> color sel forestgreen
> select #1/D:1581-2355
12078 atoms, 12219 bonds, 758 residues, 1 model selected
> color sel dodgerblue
> select #1:2401
Nothing selected
> color sel tomato
> select clear
> zone /C:2339 residueDistance 1 surfaceDistance 3 label false
Must specify a single residue, 0 specified
> show /C:786 cartoons, bonds
> color /C:786,2339 byhetero
> hide /C:786@C,O,N atoms
> volume #2 smoothingIterations 3 surfaceSmoothing true subdivideSurface true
> smoothLines true squareMesh true subdivisionLevels 2
> hide atoms
> show cartoons
> select clear
> zone /C:2339 residueDistance 1 surfaceDistance 3 label false
Must specify a single residue, 0 specified
> show /C:786 cartoons, bonds
> color /C:786,2339 byhetero
> hide /C:786@C,O,N atoms
> zone /C:786 residueDistance 1 surfaceDistance 1 label false
> ui tool show "Side View"
> clip list
Using 2 clip planes:
far offset 49.852, axis 0.768,0.427,0.477, point 208.8,224.8,278.7)
near offset 9.9946, axis -0.768,-0.427,-0.477, point 239.4,241.8,297.7)
> clip far 49.852
> clip near 9.9946
> view matrix
camera position:
0.18215,-0.058769,0.98151,386.49,-0.72751,-0.67959,0.094318,253.66,0.66148,-0.73124,-0.16654,268.95
model positions:
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0
> camera position:
> 0.54361,0.48734,0.68336,310.85,-0.83254,0.41646,0.36528,282.55,-0.10658,-0.7675,0.63213,363.31
Expected one of '360', '360sbs', '360tb', 'dome', 'mono', 'ortho', 'sbs',
'stereo', or 'tb' or a keyword
> positions:
> #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0
Unknown command: modeller positions:
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0
> clip far 49.852
> clip near 9.9946
> camera position:
> 0.54361,0.48734,0.68336,310.85,-0.83254,0.41646,0.36528,282.55,-0.10658,-0.7675,0.63213,363.31
Expected one of '360', '360sbs', '360tb', 'dome', 'mono', 'ortho', 'sbs',
'stereo', or 'tb' or a keyword
> view matrix
camera position:
0.18215,-0.058769,0.98151,386.49,-0.72751,-0.67959,0.094318,253.66,0.66148,-0.73124,-0.16654,268.95
model positions:
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0
> camera position:
> 0.54361,0.48734,0.68336,310.85,-0.83254,0.41646,0.36528,282.55,-0.10658,-0.7675,0.63213,363.31
Expected one of '360', '360sbs', '360tb', 'dome', 'mono', 'ortho', 'sbs',
'stereo', or 'tb' or a keyword
> view matrix camera
> 0.54361,0.48734,0.68336,310.85,-0.83254,0.41646,0.36528,282.55,-0.10658,-0.7675,0.63213,363.31
> models
> #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0
> clip list
Clipping is off
> close
> open /System/Volumes/Data/scicore/projects/scicore-p-maiert-
> structbio/delbartf/ACC/cryo-
> EM/Timm_reprocess/ACC_NO_citrate_real_space_refined_025-ChainC-ChainD-BUILD-
> Biotin-link_problem_no-hydrogen_Ramachandran-coot-2.pdb
Summary of feedback from opening
/System/Volumes/Data/scicore/projects/scicore-p-maiert-
structbio/delbartf/ACC/cryo-
EM/Timm_reprocess/ACC_NO_citrate_real_space_refined_025-ChainC-ChainD-BUILD-
Biotin-link_problem_no-hydrogen_Ramachandran-coot-2.pdb
---
warning | Cannot find LINK/SSBOND residue BTN (2339 )
Chain information for ACC_NO_citrate_real_space_refined_025-ChainC-ChainD-
BUILD-Biotin-link_problem_no-hydrogen_Ramachandran-coot-2.pdb #1
---
Chain | Description
B | No description available
C | No description available
D | No description available
F | No description available
> hide surfaces
> hide cartoons
> hide atoms
> show cartoons
> open /Users/delbart/delbartf/ACC/cryo-
> EM/Timm_reprocess/cryosparc_P6_J773_005_volume_map_sharp.mrc
Opened cryosparc_P6_J773_005_volume_map_sharp.mrc as #2, grid size
480,480,480, pixel 1.06, shown at level 0.0807, step 2, values float32
> volume #2 style mesh level 0.177 step 1 color snow transparency 1
> select #1/C:1-621
4077 atoms, 4173 bonds, 521 residues, 1 model selected
> color sel firebrick
> select #1/C:622-747
982 atoms, 997 bonds, 126 residues, 1 model selected
> color sel chocolate
> select #1/C:748-846
740 atoms, 752 bonds, 99 residues, 1 model selected
> color sel magenta
> select #1/C:847-1092
1981 atoms, 2014 bonds, 246 residues, 1 model selected
> color sel orange
> select #1/C:1093-1161
580 atoms, 594 bonds, 69 residues, 1 model selected
> color sel yellow
> select #1/C:1162-1376
1077 atoms, 1098 bonds, 3 pseudobonds, 129 residues, 2 models selected
> color sel yellow green
> select #1/C:1377-1581
1621 atoms, 1651 bonds, 1 pseudobond, 199 residues, 2 models selected
> color sel forestgreen
> select #1/C:1581-2355
6067 atoms, 6208 bonds, 758 residues, 1 model selected
> color sel dodgerblue
> select #1/C:2339
Nothing selected
> color sel magenta
> select #1/D:1-621
4070 atoms, 4166 bonds, 520 residues, 1 model selected
> color sel firebrick
> select #1/D:622-747
982 atoms, 997 bonds, 126 residues, 1 model selected
> color sel chocolate
> select #1/D:748-846
740 atoms, 752 bonds, 99 residues, 1 model selected
> color sel magenta
> select #1/D:847-1092
1981 atoms, 2014 bonds, 246 residues, 1 model selected
> color sel orange
> select #1/D:1093-1161
580 atoms, 594 bonds, 69 residues, 1 model selected
> color sel yellow
> select #1/D:1162-1376
1077 atoms, 1098 bonds, 3 pseudobonds, 129 residues, 2 models selected
> color sel yellow green
> select #1/D:1377-1581
1621 atoms, 1651 bonds, 1 pseudobond, 199 residues, 2 models selected
> color sel forestgreen
> select #1/D:1581-2355
6067 atoms, 6208 bonds, 758 residues, 1 model selected
> color sel dodgerblue
> select #1:2401
15 atoms, 16 bonds, 1 residue, 1 model selected
> color sel tomato
> select clear
> zone /C:2339 residueDistance 1 surfaceDistance 3 label false
Must specify a single residue, 0 specified
> zone /C:2401 residueDistance 1 surfaceDistance 3 label false
> show /C:786 cartoons, bonds
> color /C:786,2339 byhetero
> hide /C:786@C,O,N atoms
> volume #2 smoothingIterations 3 surfaceSmoothing true subdivideSurface true
> smoothLines true squareMesh true subdivisionLevels 2
> hide #1/b,f cartoons
> hide @H*
> zone /C:2401 residueDistance 1 surfaceDistance 3 label false
> show /C:786 cartoons, bonds
> color /C:786,2401 byhetero
> hide /C:786@C,O,N atoms
> volume #2 smoothingIterations 3 surfaceSmoothing true subdivideSurface true
> smoothLines true squareMesh true subdivisionLevels 2
> select #1/C:2401
15 atoms, 16 bonds, 1 residue, 1 model selected
> color sel magenta
> select #1/C:2401
15 atoms, 16 bonds, 1 residue, 1 model selected
> color sel grey
> select #1/C:2401
15 atoms, 16 bonds, 1 residue, 1 model selected
> color sel purple
> select #1/C:2401
15 atoms, 16 bonds, 1 residue, 1 model selected
> color sel magenta
> select #1/C:2401
15 atoms, 16 bonds, 1 residue, 1 model selected
> color sel salmon
> select #1/C:2401
15 atoms, 16 bonds, 1 residue, 1 model selected
> color sel wheat
> select #1/C:2401
15 atoms, 16 bonds, 1 residue, 1 model selected
> color sel wheat, byhet
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> select #1/C:2401
15 atoms, 16 bonds, 1 residue, 1 model selected
> color sel wheat, byhet
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color #1 #f5ffea transparency 0
> select #1/C:1-621
4077 atoms, 4173 bonds, 521 residues, 1 model selected
> color sel firebrick
> select #1/C:622-747
982 atoms, 997 bonds, 126 residues, 1 model selected
> color sel chocolate
> select #1/C:748-846
740 atoms, 752 bonds, 99 residues, 1 model selected
> color sel magenta
> select #1/C:847-1092
1981 atoms, 2014 bonds, 246 residues, 1 model selected
> color sel orange
> select #1/C:1093-1161
580 atoms, 594 bonds, 69 residues, 1 model selected
> color sel yellow
> select #1/C:1162-1376
1077 atoms, 1098 bonds, 3 pseudobonds, 129 residues, 2 models selected
> color sel yellow green
> select #1/C:1377-1581
1621 atoms, 1651 bonds, 1 pseudobond, 199 residues, 2 models selected
> color sel forestgreen
> select #1/C:1581-2355
6067 atoms, 6208 bonds, 758 residues, 1 model selected
> color sel dodgerblue
> select #1/C:2401
15 atoms, 16 bonds, 1 residue, 1 model selected
> color sel grey
> select #1/D:1-621
4070 atoms, 4166 bonds, 520 residues, 1 model selected
> color sel firebrick
> select #1/D:622-747
982 atoms, 997 bonds, 126 residues, 1 model selected
> color sel chocolate
> select #1/D:748-846
740 atoms, 752 bonds, 99 residues, 1 model selected
> color sel magenta
> select #1/D:847-1092
1981 atoms, 2014 bonds, 246 residues, 1 model selected
> color sel orange
> select #1/D:1093-1161
580 atoms, 594 bonds, 69 residues, 1 model selected
> color sel yellow
> select #1/D:1162-1376
1077 atoms, 1098 bonds, 3 pseudobonds, 129 residues, 2 models selected
> color sel yellow green
> select #1/D:1377-1581
1621 atoms, 1651 bonds, 1 pseudobond, 199 residues, 2 models selected
> color sel forestgreen
> select #1/D:1581-2355
6067 atoms, 6208 bonds, 758 residues, 1 model selected
> color sel dodgerblue
> select #1:2401
15 atoms, 16 bonds, 1 residue, 1 model selected
> color sel tomato
> zone /C:2401 residueDistance 1 surfaceDistance 3 label false
> show /C:786 cartoons, bonds
> color /C:786,2401 byhetero
> hide /C:786@C,O,N atoms
> color #1/C:2401 grey, byhet
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color #1/C:2401 grey, byhet
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color #1/C:2401 grey, color #1/C:2401 byhet
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color #1/C:2401 grey, color #1/C:2401 byhet
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color #1/C:2401 byhetero
> color #1/C:2401 byhet, grey
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color #1/C:2401 midnightblue
> color #1/C:2401 maroon
> color #1/C:2401 magenta
> color #1/C:2401 byhetero
> color #1/C:2401 grape
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color #1/C:2401 strawberry
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color #1/C:2401 Strawberry
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color #1 #9437ff transparency 0
> select #1/C:1-621
4077 atoms, 4173 bonds, 521 residues, 1 model selected
> color sel firebrick
> select #1/C:622-747
982 atoms, 997 bonds, 126 residues, 1 model selected
> color sel chocolate
> select #1/C:748-846
740 atoms, 752 bonds, 99 residues, 1 model selected
> color sel magenta
> select #1/C:847-1092
1981 atoms, 2014 bonds, 246 residues, 1 model selected
> color sel orange
> select #1/C:1093-1161
580 atoms, 594 bonds, 69 residues, 1 model selected
> color sel yellow
> select #1/C:1162-1376
1077 atoms, 1098 bonds, 3 pseudobonds, 129 residues, 2 models selected
> color sel yellow green
> select #1/C:1377-1581
1621 atoms, 1651 bonds, 1 pseudobond, 199 residues, 2 models selected
> color sel forestgreen
> select #1/C:1581-2355
6067 atoms, 6208 bonds, 758 residues, 1 model selected
> color sel dodgerblue
> color #1/C:2401 grey
> select #1/D:1-621
4070 atoms, 4166 bonds, 520 residues, 1 model selected
> color sel firebrick
> select #1/D:622-747
982 atoms, 997 bonds, 126 residues, 1 model selected
> color sel chocolate
> select #1/D:748-846
740 atoms, 752 bonds, 99 residues, 1 model selected
> color sel magenta
> select #1/D:847-1092
1981 atoms, 2014 bonds, 246 residues, 1 model selected
> color sel orange
> select #1/D:1093-1161
580 atoms, 594 bonds, 69 residues, 1 model selected
> color sel yellow
> select #1/D:1162-1376
1077 atoms, 1098 bonds, 3 pseudobonds, 129 residues, 2 models selected
> color sel yellow green
> select #1/D:1377-1581
1621 atoms, 1651 bonds, 1 pseudobond, 199 residues, 2 models selected
> color sel forestgreen
> select #1/D:1581-2355
6067 atoms, 6208 bonds, 758 residues, 1 model selected
> color sel dodgerblue
> select #1:2401
15 atoms, 16 bonds, 1 residue, 1 model selected
> color sel tomato
> select clear
> select #1 /C:2401
15 atoms, 16 bonds, 1 residue, 1 model selected
> color #1 #ff2f92 transparency 0
> color #1 #ff7e79 transparency 0
> color #1 #ffd479 transparency 0
> color #1 #011993 transparency 0
> color #1 #005493 transparency 0
> color #1 #00f900 transparency 0
> color #1 #00fa92 transparency 0
> color #1 #00fdff transparency 0
> color #1 #73fcd6 transparency 0
> color #1 #73fa79 transparency 0
> color #1 #73fdff transparency 0
> color #1 #76d6ff transparency 0
> color #1 #7a81ff transparency 0
> color #1 #d783ff transparency 0
> color #1 #ff85ff transparency 0
> color #1 #ff8ad8 transparency 0
> color #1 #d783ff transparency 0
> color #1 #ff85ff transparency 0
> color #1 #d783ff transparency 0
> select #1/C:1-621
4077 atoms, 4173 bonds, 521 residues, 1 model selected
> color sel firebrick
> select #1/C:622-747
982 atoms, 997 bonds, 126 residues, 1 model selected
> color sel chocolate
> select #1/C:748-846
740 atoms, 752 bonds, 99 residues, 1 model selected
> color sel magenta
> select #1/C:847-1092
1981 atoms, 2014 bonds, 246 residues, 1 model selected
> color sel orange
> select #1/C:1093-1161
580 atoms, 594 bonds, 69 residues, 1 model selected
> color sel yellow
> select #1/C:1162-1376
1077 atoms, 1098 bonds, 3 pseudobonds, 129 residues, 2 models selected
> color sel yellow green
> select #1/C:1377-1581
1621 atoms, 1651 bonds, 1 pseudobond, 199 residues, 2 models selected
> color sel forestgreen
> select #1/C:1581-2355
6067 atoms, 6208 bonds, 758 residues, 1 model selected
> color sel dodgerblue
> color #1/C:2401 grey
> select #1/D:1-621
4070 atoms, 4166 bonds, 520 residues, 1 model selected
> color sel firebrick
> select #1/D:622-747
982 atoms, 997 bonds, 126 residues, 1 model selected
> color sel chocolate
> select #1/D:748-846
740 atoms, 752 bonds, 99 residues, 1 model selected
> color sel magenta
> select #1/D:847-1092
1981 atoms, 2014 bonds, 246 residues, 1 model selected
> color sel orange
> select #1/D:1093-1161
580 atoms, 594 bonds, 69 residues, 1 model selected
> color sel yellow
> select #1/D:1162-1376
1077 atoms, 1098 bonds, 3 pseudobonds, 129 residues, 2 models selected
> color sel yellow green
> select #1/D:1377-1581
1621 atoms, 1651 bonds, 1 pseudobond, 199 residues, 2 models selected
> color sel forestgreen
> select #1/D:1581-2355
6067 atoms, 6208 bonds, 758 residues, 1 model selected
> color sel dodgerblue
> select #1:2401
15 atoms, 16 bonds, 1 residue, 1 model selected
> color sel strawberry;
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> select clear
> select #1:2401
15 atoms, 16 bonds, 1 residue, 1 model selected
> color sel Lavender;
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> select #1:2401
15 atoms, 16 bonds, 1 residue, 1 model selected
> color sel hot pink
> select #1:2401
15 atoms, 16 bonds, 1 residue, 1 model selected
> color sel dark magenta
> select #1:2401
15 atoms, 16 bonds, 1 residue, 1 model selected
> color sel purple
> select #1:2401
15 atoms, 16 bonds, 1 residue, 1 model selected
> color sel violet
> select #1:2401
15 atoms, 16 bonds, 1 residue, 1 model selected
> color sel medium violet red
> zone /C:2401 residueDistance 1 surfaceDistance 3 label false
> show /C:786 cartoons, bonds
> color /C:786,2401 byhetero
> hide /C:786@C,O,N atoms
> select clear
> view matrix
camera position:
0.35055,0.75715,0.55121,270.2,-0.76634,0.57023,-0.29591,221,-0.53836,-0.31868,0.78013,335.7
model positions:
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0
> clip list
Using 2 clip planes:
near offset 1.4108, axis -0.551,0.296,-0.780, point 242.1,236.1,295.9)
far offset 33.269, axis 0.551,-0.296,0.780, point 224.5,245.5,271)
> view matrix camera
> 0.35055,0.75715,0.55121,270.2,-0.76634,0.57023,-0.29591,221,-0.53836,-0.31868,0.78013,335.7
> models
> #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0
> clip near 1.4108 far 33.269
> save /Users/delbart/delbartf/ACC/cryo-
> EM/Timm_reprocess/ChimeraX/Biotin_lysine_test9.png pixelSize 0.01
> supersample 4 transparentBackground true
> save /System/Volumes/Data/scicore/projects/scicore-p-maiert-
> structbio/delbartf/ACC/cryo-
> EM/Timm_reprocess/ChimeraX/ACC_figures_test_session.cxs
> ui tool show "Show Sequence Viewer"
> sequence chain /C
Alignment identifier is 1/C
> select
> /C:362-364,370-372,388-390,504-508,538-540,559-564,669-676,679-686,692-697,700-707,715-717,733-736,743-746,778-784,787-792,797-801,816-820,1326-1328,1357-1359,1403-1405,1421-1423,1510-1513,1530-1533,1636-1639,1645-1648,1659-1664,1677-1682,1714-1717,1771-1774,1777-1780,1817-1820,1823-1825,1838-1840,1845-1847,1971-1978,1981-1988,1993-1996,2010-2013,2040-2042
1442 atoms, 1433 bonds, 179 residues, 1 model selected
> view #1 /C:1823
> select #1 /C:1823
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> select #1 /C:1823, show bonds
Expected a keyword
> select #1 /C:1823, style bonds
Expected a keyword
> select #1 /C:1823, style bonds
Expected a keyword
> select #1 /C:1823, style atoms
Expected a keyword
> select #1 /C:1823, style bonds
Expected a keyword
> select #1 /C:1823, style atoms
Expected a keyword
> select #1 /C:1823, bonds
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1 /C:1823, show sel atoms
Expected a keyword
> select #1 /C:1823, show sel atoms
Expected a keyword
> select #1 /C:1823 show sel atoms
Expected a keyword
> select #1 /C:1823 show atoms
Expected a keyword
> select #1 /C:1823 show atoms #1 /C:1823
Expected a keyword
> select #1 /C:1823 show #1 /C:1823 atoms
Expected a keyword
> select #1 /C:1823 show #1 /C:1823 atoms
Expected a keyword
> select #1 /C:1823, show #1 /C:1823 atoms
Expected a keyword
> select #1 /C:1823, show #1 /C:1823 bonds
Expected a keyword
> save /System/Volumes/Data/scicore/projects/scicore-p-maiert-
> structbio/delbartf/ACC/cryo-
> EM/Timm_reprocess/ChimeraX/ACC_figures_test_session.cxs
——— End of log from Fri Feb 11 17:52:40 2022 ———
opened ChimeraX session
> open /System/Volumes/Data/scicore/projects/scicore-p-maiert-
> structbio/delbartf/ACC/cryo-
> EM/Timm_reprocess/ACC_NO_citrate_real_space_refined_025-ChainC-ChainD-BUILD-
> Biotin-link_problem_no-hydrogen_Ramachandran-coot-19.pdb
Summary of feedback from opening
/System/Volumes/Data/scicore/projects/scicore-p-maiert-
structbio/delbartf/ACC/cryo-
EM/Timm_reprocess/ACC_NO_citrate_real_space_refined_025-ChainC-ChainD-BUILD-
Biotin-link_problem_no-hydrogen_Ramachandran-coot-19.pdb
---
warning | Cannot find LINK/SSBOND residue BTN (2339 )
Chain information for ACC_NO_citrate_real_space_refined_025-ChainC-ChainD-
BUILD-Biotin-link_problem_no-hydrogen_Ramachandran-coot-19.pdb #3
---
Chain | Description
B | No description available
C | No description available
D | No description available
F | No description available
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> hide #!1 models
> show #!1 models
> ui tool show "Model Panel"
> ui tool show "Side View"
> set bgColor black
> color #2 white models transparency 0
> save /Users/delbart/delbartf/ACC/cryo-
> EM/Timm_reprocess/ChimeraX/Biotin_lysine_test10.png pixelSize 0.01
> supersample 4 transparentBackground false
> select clear
> save /Users/delbart/delbartf/ACC/cryo-
> EM/Timm_reprocess/ChimeraX/Biotin_lysine_test10.png pixelSize 0.01
> supersample 4 transparentBackground false
> set bgColor white
> save /Users/delbart/delbartf/ACC/cryo-
> EM/Timm_reprocess/ChimeraX/Biotin_lysine_test11.png pixelSize 0.01
> supersample 4 transparentBackground true
[Repeated 1 time(s)]
> open /System/Volumes/Data/scicore/projects/scicore-p-maiert-
> structbio/delbartf/ACC/cryo-
> EM/Timm_reprocess/placed_model_citrate_real_space_refined.pdb
Chain information for placed_model_citrate_real_space_refined.pdb #4
---
Chain | Description
B | No description available
C D | No description available
F | No description available
> hide #!1 models
> hide #!2 models
> remove #3
Unknown command: remove #3
> delete #3
> lighting simple
> lighting soft
> show #!4 cartoons
> hide #!4 atoms
> zone #5/C:2401
Must specify a single residue, 0 specified
> zone #4/C:2401
> lighting soft
> lighting simple
> show #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> zone #2/C:2401
Must specify a single residue, 0 specified
> zone #4/C:2401
> zone #2/C:2401 residueDistance 1 surfaceDistance 3 label false
Must specify a single residue, 0 specified
> zone #4/C:2401 residueDistance 1 surfaceDistance 3 label false
> zone #4/C:2401 label false
[Repeated 1 time(s)]
> hide labels
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> zone #4/C:2401 residueDistance 1 surfaceDistance 3 label false
> ~label #1-2,4 atoms
> ~label #1-2,4 residues
> zone #4/C:2401 residueDistance 1 surfaceDistance 3 label false
> zone #4/C:2401 residueDistance 2 surfaceDistance 3 label false
> zone #4/C:2401 residueDistance 3 surfaceDistance 3 label false
> hide #!4 models
> hide #!1 models
> show #!4 models
> show #!1 models
> zone #4/C:2401 residueDistance 3 surfaceDistance 5 label false
> zone #4/C:2401 residueDistance 3 surfaceDistance 4 label false
> hide #!4 models
> show #1/C:1232,1325,1326,1359 cartoons, bonds
> color #1/C:1232,1325,1326,1359 byhetero
> hide #1/C:1232,1325,1326,1359@C,O,N atoms
> zone #4/C:2401 residueDistance 1 surfaceDistance 1 label false
> zone #4/C:2401 residueDistance 1 surfaceDistance 2 label false
> zone #4/C:2401 residueDistance 1 surfaceDistance 3 label false
> zone #4/C:2401 residueDistance 1 surfaceDistance 2 label false
> lighting full shadows false
> graphics silhouettes false width 1
> volume #2 style mesh squareMesh true subdivisionLevels 2
> volume #2 smoothingIterations 3 surfaceSmoothing true subdivideSurface true
> smoothLines true squareMesh true subdivisionLevels 2
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> save /Users/delbart/delbartf/ACC/cryo-
> EM/Timm_reprocess/ChimeraX/Arginine_citrate_test.png pixelSize 0.01
> supersample 4 transparentBackground true
> save /System/Volumes/Data/scicore/projects/scicore-p-maiert-
> structbio/delbartf/ACC/cryo-
> EM/Timm_reprocess/ChimeraX/ACC_figures_test_session_citrate_site.cxs
> close
> open /System/Volumes/Data/scicore/projects/scicore-p-maiert-
> structbio/delbartf/ACC/cryo-
> EM/Timm_reprocess/cryosparc_P6_J773_005_volume_map.mrc
Opened cryosparc_P6_J773_005_volume_map.mrc as #1, grid size 480,480,480,
pixel 1.06, shown at level 0.0686, step 2, values float32
> open /System/Volumes/Data/scicore/projects/scicore-p-maiert-
> structbio/delbartf/ACC/cryo-
> EM/Timm_reprocess/cryosparc_P6_J775_map_locres.mrc
Opened cryosparc_P6_J775_map_locres.mrc as #2, grid size 480,480,480, pixel
1.06, shown at level 0.000418, step 2, values float32
> volume #1 step 1
> volume #1 level 0.0567
> hide #!2 models
> volume #1 level 0.1445
> volume #2 step 1
> ui tool show "Color Zone"
> ui tool show "Surface Color"
> key red-white-blue :0.0 :0.5 :1.0 showTool true
> ui mousemode right "color key"
> ui mousemode right translate
> color sample #1.1 map #2 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000
Map values for surface "surface": minimum 0, mean 3.553, maximum 7.338
> key rainbow :0.00 :1.83 :3.67 :5.50 :7.34 showTool true
> ui mousemode right "color key"
> ui mousemode right translate
> color sample #1.1 map #2 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000
Map values for surface "surface": minimum 0, mean 3.553, maximum 7.338
> toolshed show
[Repeated 1 time(s)]
> ui tool show "Map Statistics"
> measure mapstats #!1
Map cryosparc_P6_J773_005_volume_map.mrc #1, minimum -0.4327, maximum 0.7899,
mean -0.0001257, SD 0.01603, RMS 0.01603
> color sample #1.1 map #2 palette
> 2,#0000ff:3,#00ffff:4,#00ff00:5,#ffff00:6,#ff0000
Map values for surface "surface": minimum 0, mean 3.553, maximum 7.338
> key rainbow :2 :3 :4 :5 :6 showTool true
> ui mousemode right "color key"
> ui mousemode right translate
> key rainbow :2.5 :3.5 :4.5 :5.5 :6.5 showTool true
> ui mousemode right "color key"
> ui mousemode right translate
> color sample #1.1 map #2 palette
> 2.5,#0000ff:3.5,#00ffff:4.5,#00ff00:5.5,#ffff00:6.5,#ff0000
Map values for surface "surface": minimum 0, mean 3.553, maximum 7.338
> color sample #1.1 map #2 palette
> 3,#0000ff:4,#00ffff:5,#00ff00:6,#ffff00:7,#ff0000
Map values for surface "surface": minimum 0, mean 3.553, maximum 7.338
> color sample #1.1 map #2 palette
> 2.5,#0000ff:3.5,#00ffff:4.5,#00ff00:5.5,#ffff00:6.5,#ff0000
Map values for surface "surface": minimum 0, mean 3.553, maximum 7.338
> key rainbow :2.5 :3.5 :4.5 :5.5 :6.5 showTool true
> ui mousemode right "color key"
> key blue:2.5 cyan:3.5
> key blue:2.5 cyan:3.5 white: white: white:
> ui mousemode right translate
> key rainbow :2.5 :3.5 :4.5 :5.5 :6.5 showTool true
> ui mousemode right "color key"
> ui mousemode right translate
> key rainbow :2.5 :3.5 :4.5 :5.5 :6.5 showTool true
> ui mousemode right "color key"
> key rainbow :2.5 :3.5 :4.5 : :6.5
> key rainbow :2.5 :3.5 : : :6.5
> key rainbow :2.5 : : : :6.5
> ui mousemode right translate
> volume #1 level 0.113
> color sample #1.1 map #2 palette
> 2.5,#0000ff:3.5,#00ffff:4.5,#00ff00:5.5,#ffff00:6.5,#ff0000
Map values for surface "surface": minimum 0, mean 3.194, maximum 7.398
> color sample #1.1 map #2 palette
> 2.5,#0000ff:3.5,#00ffff:4.5,#00ff00:5.5,#ffff00:6.5,#ff0000
Map values for surface "surface": minimum 0, mean 3.194, maximum 7.398
> volume #1 level 0.1366
> volume #1 level 0.177
> volume #1 level 0.147
> save /Users/delbart/delbartf/ACC/cryo-
> EM/Timm_reprocess/ChimeraX/Localresmap.png pixelSize 0.01 supersample 4
> transparentBackground true
Image size 29873 x 25095 too large, exceeds maximum OpenGL render buffer size
16384
> save /Users/delbart/delbartf/ACC/cryo-
> EM/Timm_reprocess/ChimeraX/Localresmap.png pixelSize 0.1 supersample 4
> transparentBackground true
> volume #1 smoothingIterations 3 surfaceSmoothing true subdivideSurface true
> smoothLines true
> volume #1 smoothingIterations 4 surfaceSmoothing true subdivideSurface true
> smoothLines true
> lighting soft
> lighting simple
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting shadows false
> lighting shadows true
> lighting full
> lighting soft
> lighting shadows true intensity 0.5
> graphics silhouettes true
> volume #1 smoothingIterations 4 surfaceSmoothing true subdivideSurface true
> smoothLines true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true
> lighting shadows false
> save /Users/delbart/delbartf/ACC/cryo-
> EM/Timm_reprocess/ChimeraX/Localresmap1.png pixelSize 0.1 supersample 4
> transparentBackground true
> set bgColor black
> graphics silhouettes false
> graphics silhouettes true
> save /System/Volumes/Data/scicore/projects/scicore-p-maiert-
> structbio/delbartf/ACC/cryo-
> EM/Timm_reprocess/ChimeraX/ACC_Cit_localresmap.cxs
——— End of log from Tue Feb 15 19:16:03 2022 ———
opened ChimeraX session
> toolshed show
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 2251, in <lambda>
dw.closeEvent = lambda e, *, tw=tool_window, mw=mw: mw.close_request(tw, e)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 654, in close_request
tool_instance.delete()
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seq-view/tool.py", line 511, in delete
self.alignment.detach_viewer(self)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/alignment.py", line 398, in detach_viewer
self.session.alignments.destroy_alignment(self)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/manager.py", line 117, in destroy_alignment
del self._alignments[alignment.ident]
KeyError: '3'
KeyError: '3'
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/manager.py", line 117, in destroy_alignment
del self._alignments[alignment.ident]
See log for complete Python traceback.
> ui tool show "Selection Inspector"
> view #1 clip false
No atomic structure models chosen
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #3 models
> show #3 models
> hide #!2 models
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 1700, in _update_running_tools
tool_action.setToolTip("%s %s tool" % (("Hide" if tw.shown else "Show"),
tw.title))
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 2090, in shown
return self.__toolkit.shown
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 2390, in shown
return not self.dock_widget.isHidden()
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 2390, in shown
return not self.dock_widget.isHidden()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 1700, in _update_running_tools
tool_action.setToolTip("%s %s tool" % (("Hide" if tw.shown else "Show"),
tw.title))
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 2090, in shown
return self.__toolkit.shown
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 2390, in shown
return not self.dock_widget.isHidden()
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 2390, in shown
return not self.dock_widget.isHidden()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 1700, in _update_running_tools
tool_action.setToolTip("%s %s tool" % (("Hide" if tw.shown else "Show"),
tw.title))
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 2090, in shown
return self.__toolkit.shown
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 2390, in shown
return not self.dock_widget.isHidden()
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 2390, in shown
return not self.dock_widget.isHidden()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 1700, in _update_running_tools
tool_action.setToolTip("%s %s tool" % (("Hide" if tw.shown else "Show"),
tw.title))
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 2090, in shown
return self.__toolkit.shown
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 2390, in shown
return not self.dock_widget.isHidden()
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 2390, in shown
return not self.dock_widget.isHidden()
See log for complete Python traceback.
OpenGL version: 4.1 INTEL-18.4.6
OpenGL renderer: Intel(R) Iris(TM) Pro Graphics 6200
OpenGL vendor: Intel Inc.Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac16,2
Processor Name: Quad-Core Intel Core i5
Processor Speed: 3.1 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 4 MB
Memory: 16 GB
System Firmware Version: 428.60.3.0.0
OS Loader Version: 540.80.2~11
SMC Version (system): 2.32f21
Software:
System Software Overview:
System Version: macOS 12.2.1 (21D62)
Kernel Version: Darwin 21.3.0
Time since boot: 4 days 23:30
Graphics/Displays:
Intel Iris Pro Graphics 6200:
Chipset Model: Intel Iris Pro Graphics 6200
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x1622
Revision ID: 0x000a
Metal Family: Supported, Metal GPUFamily macOS 1
Displays:
DELL P2217H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: RH81R67C59DB
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: Yes
Connection Type: Thunderbolt/DisplayPort
iMac:
Display Type: Built-In Retina LCD
Resolution: 4096 x 2304 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 5A0210B34E125
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.5.30
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.0
ParmEd: 3.2.0
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 4 years ago
| Component: | Unassigned → Sequence |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Sequence viewer not tracked by alignments manager |
comment:2 by , 4 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
Note:
See TracTickets
for help on using tickets.
