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#7021 closed defect (not a bug)
Save TIFF, not TIFF stack
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| 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
I was trying to save the image as tif, it kept giving me this error message: 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/toolbar/tool.py", line 165, in callback
bundle_info.run_provider(session, name, session.toolbar, display_name=display_name)
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/toolshed/info.py", line 381, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/toolshed/__init__.py", line 1284, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/toolbar/__init__.py", line 37, in run_provider
providers.run_provider(session, name)
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/toolbar/providers.py", line 45, in run_provider
what(session)
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/toolbar/providers.py", line 27, in _file_save
show_save_file_dialog(session)
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/save_command/dialog.py", line 51, in display
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/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
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/save_command/cmd.py", line 89, in provider_save
saver_info.save(session, path, **provider_kw)
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/map/__init__.py", line 185, in save
save_map(session, path, _name, **kw)
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/map/volume.py", line 3972, in save_map
save_grid_data(grids, path, session, format_name, options)
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/map_data/fileformats.py", line 314, in save_grid_data
ff.save_func(garg, tpath, options = options, progress = p)
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/map_data/imagestack/imagej_write.py", line 19, in write_imagej_tiff
_write_3d_tiff(grid_data, path)
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/map_data/imagestack/imagej_write.py", line 29, in _write_3d_tiff
imwrite(path, array_zcyx, imagej=True, resolution=(1/xstep, 1/ystep),
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/tifffile/tifffile.py", line 856, in imwrite
result = tif.write(data, shape, dtype, **kwargs)
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/tifffile/tifffile.py", line 1640, in write
ijshape = imagej_shape(
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/tifffile/tifffile.py", line 14066, in imagej_shape
raise ValueError('ImageJ hyperstack shape and axes do not match')
ValueError: ImageJ hyperstack shape and axes do not match
ValueError: ImageJ hyperstack shape and axes do not match
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/tifffile/tifffile.py", line 14066, in imagej_shape
raise ValueError('ImageJ hyperstack shape and axes do not match')
See log for complete Python traceback.
It worked before, but just started to happen since yesterday. I am not sure why. Thanks.
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/jl209164/OneDrive -
> GSK/Documents/IPTc&developmentPlan/GSK-R&Dday/2022/gB-4H9-interfaceconservation/gB-
> surface_0602.cxs" format session
Log from Thu Jun 2 10:58:00 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/jl209164/OneDrive -
> GSK/Documents/IPTc&developmentPlan/GSK-R&Dday/2022/gB-
> surface_sequenceconservation.cxs" format session
Log from Wed Jun 1 11:14:26 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/jl209164/Library/CloudStorage/OneDrive-GSK/Documents/CMV-
> related/CMV/gB-4H9-paper/gB-4H9-seq-conservationFeb24.cxs format session
Log from Thu Feb 24 15:44:07 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/jl209164/Library/CloudStorage/OneDrive-GSK/Documents/CMV-
> related/CMV/gB-4H9modeling/gB-mutants-4H9binding.cxs format session
Log from Wed Feb 9 13:51:56 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/jingliu/Documents/CMV/gB-4H9modeling/RealSpaceRefine_7/gB-4H9_rmC_Jan312022_real_space_refined_007.pdb
Chain information for gB-4H9_rmC_Jan312022_real_space_refined_007.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
T W Y | No description available
U V X | No description available
> ui tool show "Show Sequence Viewer"
> ui tool show "Surface Color"
> toolshed show
> select /A
9220 atoms, 9334 bonds, 2 pseudobonds, 572 residues, 2 models selected
> ui tool show "Blast Protein"
> blastprotein /A database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 name
> bp1
Web Service: BlastProtein2 is a Python wrapper that calls blastp to search nr
or pdb for sequences similar to the given protein sequence
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/BlastProtein2Service
Opal job id: appBlastProtein2Service1643742260304-38379452
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appBlastProtein2Service1643742260304-38379452
stdout.txt = standard output
stderr.txt = standard error
BlastProtein finished.
> ui tool show "Color Actions"
> ui tool show "Color Key"
> ui mousemode left "color key"
> ui mousemode left rotate
> close #2
> close
> fetch 121p
Unknown command: fetch 121p
> fetch 121P
Unknown command: fetch 121P
> open 121P
Summary of feedback from opening 121P fetched from pdb
---
notes | Fetching compressed mmCIF 121p from
http://files.rcsb.org/download/121p.cif
Fetching CCD MG from http://ligand-expo.rcsb.org/reports/M/MG/MG.cif
Fetching CCD GCP from http://ligand-expo.rcsb.org/reports/G/GCP/GCP.cif
121p title:
Struktur und guanosintriphosphat-hydrolysemechanismus des C-terminal
verkuerzten menschlichen krebsproteins P21-H-ras [more info...]
Chain information for 121p #1
---
Chain | Description
A | H-ras P21 protein
Non-standard residues in 121p #1
---
GCP — phosphomethylphosphonic acid guanylate ester
MG — magnesium ion
121p mmCIF Assemblies
---
1| author_defined_assembly
> hide solvent
> style ligand ball
Changed 32 atom styles
> open https://www.rbvi.ucsf.edu/chimerax/data/conservation-
> coloring/121p-consurf.aln
Summary of feedback from opening
//www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/121p-consurf.aln
fetched from https
---
notes | Fetching 121p-consurf.aln from
https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/121p-consurf.aln
Downloaded 121p-consurf.aln to /Users/jingliu/Downloads/121p-consurf.aln
Alignment identifier is 121p-consurf.aln
Associated 121p chain A to Input_pdb_SEQRES_A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment 121p-consurf.aln
Opened 150 sequences from 121p-consurf.aln
> color byattribute seq_conservation
1550 atoms, 363 residues, atom seq_conservation range -1.47 to 2.83
> color byattribute seq_conservation palette blue:red:yellow
1550 atoms, 363 residues, atom seq_conservation range -1.47 to 2.83
> color byattribute seq_conservation palette cyanmaroon
1550 atoms, 363 residues, atom seq_conservation range -1.47 to 2.83
> color byattribute seq_conservation palette cyanmaroon range -1.4, 1.4
1550 atoms, 363 residues, atom seq_conservation range -1.47 to 2.83
> hide protein
> show ::seq_conservation>1.8
> label ::seq_consservation>1.8
> label height 1.3
Label command requires an atom specifier to create labels.
> preset inter
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
> close session
> open 3sn6
Summary of feedback from opening 3sn6 fetched from pdb
---
notes | Fetching compressed mmCIF 3sn6 from
http://files.rcsb.org/download/3sn6.cif
Fetching CCD P0G from http://ligand-expo.rcsb.org/reports/P/P0G/P0G.cif
3sn6 title:
Crystal structure of the beta2 adrenergic receptor-Gs protein complex [more
info...]
Chain information for 3sn6 #1
---
Chain | Description
A | Guanine nucleotide-binding protein G(s) subunit α isoforms short
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
N | Camelid antibody VHH fragment
R | Endolysin,Beta-2 adrenergic receptor
Non-standard residues in 3sn6 #1
---
P0G —
8-[(1R)-2-{[1,1-dimethyl-2-(2-methylphenyl)ethyl]amino}-1-hydroxyethyl]-5-hydroxy-2H-1,4-benzoxazin-3(4H)-one
> preset cylinders
Changed 10247 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> color /R yellow
> hide /N cartoons
> open https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/81321.ali
Summary of feedback from opening
//www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/81321.ali fetched from
https
---
notes | Fetching 81321.ali from
https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/81321.ali
Downloaded 81321.ali to /Users/jingliu/Downloads/81321.ali
Alignment identifier is 81321.ali
Showing conservation header ("seq_conservation" residue attribute) for
alignment 81321.ali
Opened 10 sequences from 81321.ali
> sequence associate /R 81321.ali
Associated 3sn6 chain R to d2rh1a1 with 2 mismatches and/or gaps
> color byattribute seq_conservation /R & protein range -1.5,3 noValueColor
> gray
3433 atoms, 443 residues, atom seq_conservation range -1.76 to 4.75
> show ::seq_conservation>2
> size stickRadius .5
Changed 10478 bond radii
> color ligand byhetero
> lighting simple
> close session
> open 1kmo
Summary of feedback from opening 1kmo fetched from pdb
---
notes | Fetching compressed mmCIF 1kmo from
http://files.rcsb.org/download/1kmo.cif
Fetching CCD LDA from http://ligand-expo.rcsb.org/reports/L/LDA/LDA.cif
Fetching CCD HTO from http://ligand-expo.rcsb.org/reports/H/HTO/HTO.cif
1kmo title:
Crystal structure of the Outer Membrane Transporter FecA [more info...]
Chain information for 1kmo #1
---
Chain | Description
A | Iron(III) dicitrate transport protein fecA
Non-standard residues in 1kmo #1
---
HTO — heptane-1,2,3-triol
LDA — lauryl dimethylamine-N-oxide
> hide
> open https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/56935.ali
Summary of feedback from opening
//www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/56935.ali fetched from
https
---
notes | Fetching 56935.ali from
https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/56935.ali
Downloaded 56935.ali to /Users/jingliu/Downloads/56935.ali
Alignment identifier is 56935.ali
Associated 1kmo chain A to d1kmoa- with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment 56935.ali
Opened 13 sequences from 56935.ali
> select ~::seq_conservation
2540 atoms, 2197 bonds, 653 residues, 1 model selected
> open
> /Users/jingliu/Documents/CMV/gB-4H9modeling/RealSpaceRefine_7/gB-4H9_rmC_Jan312022_real_space_refined_007.pdb
Chain information for gB-4H9_rmC_Jan312022_real_space_refined_007.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
T W Y | No description available
U V X | No description available
> open /Users/jingliu/Documents/CMV/gB-4H9modeling/gBsequnce_UniprotKB.fasta
Sequence 'tr|A8T7D5|A8T7D5_HCMV Envelope glycoprotein B OS=Human
cytomegalovirus OX=10359 GN=UL55 PE=1 SV=1\' differs in length from preceding
sequences, and it is therefore impossible to open these sequences as an
alignment. If you want to open the sequences individually, specify 'false' as
the value of the 'alignment' keyword in the 'open' command.
> close session
> open
> /Users/jingliu/Documents/CMV/gB-4H9modeling/RealSpaceRefine_7/gB-4H9_rmC_Jan312022_real_space_refined_007.pdb
Chain information for gB-4H9_rmC_Jan312022_real_space_refined_007.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
T W Y | No description available
U V X | No description available
> open /Users/jingliu/Documents/CMV/gB-4H9modeling/gBsequnce_UniprotKB.fasta
Sequence 'tr|A8T7D5|A8T7D5_HCMV Envelope glycoprotein B OS=Human
cytomegalovirus OX=10359 GN=UL55 PE=1 SV=1\' differs in length from preceding
sequences, and it is therefore impossible to open these sequences as an
alignment. If you want to open the sequences individually, specify 'false' as
the value of the 'alignment' keyword in the 'open' command.
> open
> /Users/jingliu/Documents/CMV/gB-4H9modeling/gB_sequencealignmentresult.aln
Traceback (most recent call last):
File
"/Users/jingliu/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/parse.py", line 31, in open_file
seqs, file_attrs, file_markups = ns['read'](session, stream)
File
"/Users/jingliu/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/io/readALN.py", line 33, in read
raise FormatSyntaxError("First non-blank line does not start with 'CLUSTAL'")
chimerax.seqalign.parse.FormatSyntaxError: First non-blank line does not start
with 'CLUSTAL'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Users/jingliu/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 261, in event
_open_dropped_file(self.session, event.file())
File
"/Users/jingliu/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 1812, in _open_dropped_file
run(session, 'open %s' % FileNameArg.unparse(path))
File
"/Users/jingliu/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Users/jingliu/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Users/jingliu/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
"/Users/jingliu/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Users/jingliu/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 179, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File
"/Users/jingliu/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 421, in collated_open
return func(*func_args, **func_kw)
File
"/Users/jingliu/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/__init__.py", line 61, in open
return open_file(session, data, file_name,
File
"/Users/jingliu/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/parse.py", line 33, in open_file
raise IOError("Syntax error in %s file '%s': %s" % (format_name, fname, err))
OSError: Syntax error in ALN file 'gB_sequencealignmentresult.aln': First non-
blank line does not start with 'CLUSTAL'
OSError: Syntax error in ALN file 'gB_sequencealignmentresult.aln': First non-
blank line does not start with 'CLUSTAL'
File
"/Users/jingliu/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/parse.py", line 33, in open_file
raise IOError("Syntax error in %s file '%s': %s" % (format_name, fname, err))
See log for complete Python traceback.
> open
> /Users/jingliu/Documents/CMV/gB-4H9modeling/gB_sequencealignmentresult.aln
Traceback (most recent call last):
File
"/Users/jingliu/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/parse.py", line 31, in open_file
seqs, file_attrs, file_markups = ns['read'](session, stream)
File
"/Users/jingliu/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/io/readALN.py", line 33, in read
raise FormatSyntaxError("First non-blank line does not start with 'CLUSTAL'")
chimerax.seqalign.parse.FormatSyntaxError: First non-blank line does not start
with 'CLUSTAL'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Users/jingliu/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 261, in event
_open_dropped_file(self.session, event.file())
File
"/Users/jingliu/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 1812, in _open_dropped_file
run(session, 'open %s' % FileNameArg.unparse(path))
File
"/Users/jingliu/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Users/jingliu/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Users/jingliu/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
"/Users/jingliu/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Users/jingliu/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 179, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File
"/Users/jingliu/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 421, in collated_open
return func(*func_args, **func_kw)
File
"/Users/jingliu/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/__init__.py", line 61, in open
return open_file(session, data, file_name,
File
"/Users/jingliu/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/parse.py", line 33, in open_file
raise IOError("Syntax error in %s file '%s': %s" % (format_name, fname, err))
OSError: Syntax error in ALN file 'gB_sequencealignmentresult.aln': First non-
blank line does not start with 'CLUSTAL'
OSError: Syntax error in ALN file 'gB_sequencealignmentresult.aln': First non-
blank line does not start with 'CLUSTAL'
File
"/Users/jingliu/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/parse.py", line 33, in open_file
raise IOError("Syntax error in %s file '%s': %s" % (format_name, fname, err))
See log for complete Python traceback.
> open
> /Users/jingliu/Documents/CMV/gB-4H9modeling/gB_sequencealignmentresult.clustal
Traceback (most recent call last):
File
"/Users/jingliu/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/parse.py", line 31, in open_file
seqs, file_attrs, file_markups = ns['read'](session, stream)
File
"/Users/jingliu/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/io/readALN.py", line 33, in read
raise FormatSyntaxError("First non-blank line does not start with 'CLUSTAL'")
chimerax.seqalign.parse.FormatSyntaxError: First non-blank line does not start
with 'CLUSTAL'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Users/jingliu/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 261, in event
_open_dropped_file(self.session, event.file())
File
"/Users/jingliu/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 1812, in _open_dropped_file
run(session, 'open %s' % FileNameArg.unparse(path))
File
"/Users/jingliu/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Users/jingliu/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Users/jingliu/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
"/Users/jingliu/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Users/jingliu/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 179, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File
"/Users/jingliu/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 421, in collated_open
return func(*func_args, **func_kw)
File
"/Users/jingliu/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/__init__.py", line 61, in open
return open_file(session, data, file_name,
File
"/Users/jingliu/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/parse.py", line 33, in open_file
raise IOError("Syntax error in %s file '%s': %s" % (format_name, fname, err))
OSError: Syntax error in ALN file 'gB_sequencealignmentresult.clustal': First
non-blank line does not start with 'CLUSTAL'
OSError: Syntax error in ALN file 'gB_sequencealignmentresult.clustal': First
non-blank line does not start with 'CLUSTAL'
File
"/Users/jingliu/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/parse.py", line 33, in open_file
raise IOError("Syntax error in %s file '%s': %s" % (format_name, fname, err))
See log for complete Python traceback.
> open /Users/jingliu/Downloads/56935.ali
Summary of feedback from opening /Users/jingliu/Downloads/56935.ali
---
notes | Alignment identifier is 56935.ali
Showing conservation header ("seq_conservation" residue attribute) for
alignment 56935.ali
Opened 13 sequences from 56935.ali
> open
> /Users/jingliu/Downloads/clustalo-E20220201-203645-0832-69670873-p1m.clustal
Summary of feedback from opening
/Users/jingliu/Downloads/clustalo-E20220201-203645-0832-69670873-p1m.clustal
---
notes | Alignment identifier is
clustalo-E20220201-203645-0832-69670873-p1m.clustal
Associated gB-4H9_rmC_Jan312022_real_space_refined_007.pdb chain C to
tr|A0A3G6XLA9|A0A3G6XLA9_HCMV with 6 mismatches
Associated gB-4H9_rmC_Jan312022_real_space_refined_007.pdb chain B to
tr|A0A3G6XLA9|A0A3G6XLA9_HCMV with 6 mismatches
Associated gB-4H9_rmC_Jan312022_real_space_refined_007.pdb chain A to
tr|A0A3G6XLA9|A0A3G6XLA9_HCMV with 6 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment clustalo-E20220201-203645-0832-69670873-p1m.clustal
Opened 109 sequences from clustalo-E20220201-203645-0832-69670873-p1m.clustal
> sequence associate /A clustalo-E20220201-203645-0832-69670873-p1m.clustal
Disassociated gB-4H9_rmC_Jan312022_real_space_refined_007.pdb chain A from
tr|A0A3G6XLA9|A0A3G6XLA9_HCMV
Associated gB-4H9_rmC_Jan312022_real_space_refined_007.pdb chain A to
tr|A0A3G6XLA9|A0A3G6XLA9_HCMV with 6 mismatches
> sequence associate /A clustalo-E20220201-203645-0832-69670873-p1m.clustal
Disassociated gB-4H9_rmC_Jan312022_real_space_refined_007.pdb chain A from
tr|A0A3G6XLA9|A0A3G6XLA9_HCMV
Associated gB-4H9_rmC_Jan312022_real_space_refined_007.pdb chain A to
tr|A0A3G6XLA9|A0A3G6XLA9_HCMV with 6 mismatches
> color byattribute seq_conservation
38352 atoms, 2437 residues, atom seq_conservation range -3.69 to 0.439
> cartoon
> hide target a
> color byattribute seq_conservation palette cyanmaroon
38352 atoms, 2437 residues, atom seq_conservation range -3.69 to 0.439
> color byattribute seq_conservation
38352 atoms, 2437 residues, atom seq_conservation range -3.69 to 0.439
> select /C,B,A:347-348
102 atoms, 102 bonds, 6 residues, 1 model selected
> select /C,B,A:347-387
1914 atoms, 1932 bonds, 123 residues, 1 model selected
> select clear
> open 7kdd
7kdd title:
HCMV postfusion gB in complex with SM5-1 Fab [more info...]
Chain information for 7kdd #2
---
Chain | Description
A B C | Envelope glycoprotein B
D F H | SM5-1 Fab antibody heavy chain
E G I | SM5-1 Fab antibody light chain
Non-standard residues in 7kdd #2
---
CA — calcium ion
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
Associated 7kdd chain A to tr|A0A0G2TK23|A0A0G2TK23_HCMV with 0 mismatches
Associated 7kdd chain B to tr|A0A0G2TK23|A0A0G2TK23_HCMV with 0 mismatches
Associated 7kdd chain C to tr|A0A0G2TK23|A0A0G2TK23_HCMV with 0 mismatches
> ui tool show Matchmaker
> matchmaker #!1 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 7kdd, chain A (#2) with
gB-4H9_rmC_Jan312022_real_space_refined_007.pdb, chain B (#1), sequence
alignment score = 2603.9
RMSD between 495 pruned atom pairs is 1.154 angstroms; (across all 566 pairs:
2.218)
> hide target a
> select #2/D
998 atoms, 1020 bonds, 131 residues, 1 model selected
> cartoon sel
> select #2/E
796 atoms, 813 bonds, 110 residues, 1 model selected
> cartoon sel
> select clear
> open 5c6t
Summary of feedback from opening 5c6t fetched from pdb
---
note | Fetching compressed mmCIF 5c6t from
http://files.rcsb.org/download/5c6t.cif
5c6t title:
Crystal structure of HCMV glycoprotein B in complex with 1G2 Fab [more
info...]
Chain information for 5c6t #3
---
Chain | Description
A | Envelope glycoprotein B
H | 1G2 Fab heavy chain
L | 1G2 Fab light chain
Non-standard residues in 5c6t #3
---
MG — magnesium ion
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose
5c6t mmCIF Assemblies
---
1| author_and_software_defined_assembly
Associated 5c6t chain A to tr|A0A5S9BIY9|A0A5S9BIY9_HCMV with 30 mismatches
> ui tool show Matchmaker
> matchmaker #!1 to #3
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 5c6t, chain A (#3) with
gB-4H9_rmC_Jan312022_real_space_refined_007.pdb, chain B (#1), sequence
alignment score = 2561.2
RMSD between 422 pruned atom pairs is 0.867 angstroms; (across all 559 pairs:
2.493)
> ui tool show Matchmaker
> matchmaker #!1 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 7kdd, chain A (#2) with
gB-4H9_rmC_Jan312022_real_space_refined_007.pdb, chain B (#1), sequence
alignment score = 2603.9
RMSD between 495 pruned atom pairs is 1.154 angstroms; (across all 566 pairs:
2.218)
> ui tool show Matchmaker
> matchmaker #!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 gB-4H9_rmC_Jan312022_real_space_refined_007.pdb, chain B (#1) with
5c6t, chain A (#3), sequence alignment score = 2561.2
RMSD between 422 pruned atom pairs is 0.867 angstroms; (across all 559 pairs:
2.493)
> select #3/A
4688 atoms, 4799 bonds, 6 pseudobonds, 575 residues, 3 models selected
> cartoon hide (#!3 & sel)
> select clear
> select #3/A
4688 atoms, 4799 bonds, 6 pseudobonds, 575 residues, 3 models selected
> hide (#!3 & sel) target a
> set bgColor white
> select #3/A:181
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:181-182
16 atoms, 16 bonds, 2 residues, 1 model selected
> show ::seq_conservation<-1
> show ::seq_conservation<-1.5
> hide ::seq_conservation>-1.8
> hide ::seq_conservation<-1.8
> show ::seq_conservation<-1.8
> label ::seq_conservation<-1.8
> label height 3
> select #2/A#2/B#2/C#3/A
19047 atoms, 19511 bonds, 15 pseudobonds, 2319 residues, 6 models selected
> cartoon hide (#!2-3 & sel)
> label (#!2-3 & sel) attribute label_one_letter_code
> hide label
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> ~label (#!2-3 & sel) residues
> select #1/A
9220 atoms, 9334 bonds, 2 pseudobonds, 572 residues, 2 models selected
> ~label (#!1 & sel) residues
> select #1/B
9317 atoms, 9432 bonds, 2 pseudobonds, 577 residues, 2 models selected
> ~label (#!1 & sel) residues
> select #1/C
9399 atoms, 9515 bonds, 2 pseudobonds, 583 residues, 2 models selected
> ~label (#!1 & sel) residues
> select clear
> hide target a
> show sidechain target ab
> hide target a
> color byattribute seq_conservation range -3.69, 0.39
64501 atoms, 5698 residues, atom seq_conservation range -4.36 to 0.439
> color byattribute seq_conservation palette cyanmaroon
64501 atoms, 5698 residues, atom seq_conservation range -4.36 to 0.439
> color byattribute seq_conservation palette cyanmaroon range -4, 2
64501 atoms, 5698 residues, atom seq_conservation range -4.36 to 0.439
> color byattribute seq_conservation range -4, 2
64501 atoms, 5698 residues, atom seq_conservation range -4.36 to 0.439
> show ::seq_conservation<-1.8
> select #3/H
908 atoms, 935 bonds, 1 pseudobond, 113 residues, 2 models selected
> color (#!3 & sel) yellow
> select #3/L
784 atoms, 805 bonds, 104 residues, 1 model selected
> color sel yellow
> ui tool show "Color Actions"
> color sel gold
> select clear
> color byattribute seq_conservation
64501 atoms, 5698 residues, atom seq_conservation range -4.36 to 0.439
> color byattribute seq_conservation palette blue:red:yellow
64501 atoms, 5698 residues, atom seq_conservation range -4.36 to 0.439
> select #3/H
908 atoms, 935 bonds, 1 pseudobond, 113 residues, 2 models selected
> color sel fire brick
> color sel chartreuse
> color sel olive
> color sel peru
> color sel medium turquoise
> color sel brown
> color sel sienna
> select #3/L
784 atoms, 805 bonds, 104 residues, 1 model selected
> color sel coral
> color sel indian red
> color sel lime green
> color sel olive
> color sel dark salmon
> color sel salmon
> color sel peru
> color sel light salmon
> color sel dark goldenrod
> color sel yellow green
> select clear
> color byattribute seq_conservation palette blue:red:white
64501 atoms, 5698 residues, atom seq_conservation range -4.36 to 0.439
> color byattribute seq_conservation palette blue:red:yellow
64501 atoms, 5698 residues, atom seq_conservation range -4.36 to 0.439
> select #1/A
9220 atoms, 9334 bonds, 2 pseudobonds, 572 residues, 2 models selected
> surface (#!1 & sel)
> cartoon hide (#!1 & sel)
> surface hidePatches (#!1 & sel)
> cartoon (#!1 & sel)
> select clear
> windowsize 400 400
> windowsize 600 600
> lighting flat
> lighting simple
> lighting simple
> lighting soft
> lighting full
> lighting simple
> set bgColor black
> set bgColor white
> lighting flat
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> graphics silhouettes true
> lighting full
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting simple
> lighting soft
> ui tool show "Side View"
> view
> view
> view orient
> save /Users/jingliu/Documents/gB_sequenceconservationcolor_Feb1.png width
> 600 height 600 supersample 3
> select #1/V
1882 atoms, 1910 bonds, 123 residues, 1 model selected
> cartoon hide sel
> select #1/W
1590 atoms, 1611 bonds, 112 residues, 1 model selected
> cartoon hide sel
> select #1/X
1882 atoms, 1910 bonds, 123 residues, 1 model selected
> cartoon hide sel
> select #1/Y
1590 atoms, 1611 bonds, 112 residues, 1 model selected
> cartoon hide sel
> select #3/H
908 atoms, 935 bonds, 1 pseudobond, 113 residues, 2 models selected
> cartoon hide (#!3 & sel)
> select #3/L
784 atoms, 805 bonds, 104 residues, 1 model selected
> cartoon hide sel
> select #2/D#2/F#2/H
2994 atoms, 3060 bonds, 393 residues, 1 model selected
> cartoon hide sel
> select #2/E#2/G#2/I
2388 atoms, 2439 bonds, 330 residues, 1 model selected
> cartoon hide sel
> save /Users/jingliu/Documents/gB_seq_conservation_4H9.png width 781 height
> 705 supersample 3
> select #3/H
908 atoms, 935 bonds, 1 pseudobond, 113 residues, 2 models selected
> cartoon (#!3 & sel)
> select #3/L
784 atoms, 805 bonds, 104 residues, 1 model selected
> cartoon sel
> select clear
> save /Users/jingliu/Documents/gB_seq_conservation_with1G2.png width 781
> height 705 supersample 3
> select #2/D
998 atoms, 1020 bonds, 131 residues, 1 model selected
> cartoon sel
> select #2/E
796 atoms, 813 bonds, 110 residues, 1 model selected
> cartoon sel
> select clear
> select #2/E
796 atoms, 813 bonds, 110 residues, 1 model selected
> select #2/D
998 atoms, 1020 bonds, 131 residues, 1 model selected
> hide sel target a
> style sel stick
Changed 998 atom styles
> select #2/A
4787 atoms, 4904 bonds, 3 pseudobonds, 582 residues, 3 models selected
> hide (#!2 & sel) target a
> select #3/A
4688 atoms, 4799 bonds, 6 pseudobonds, 575 residues, 3 models selected
> hide (#!3 & sel) target a
> save /Users/jingliu/Documents/gB_seq_conservation_withSM5.png width 781
> height 705 supersample 3
> select #1/C,B,A:275
63 atoms, 63 bonds, 3 residues, 1 model selected
> lighting full
> lighting soft
> lighting full
> lighting simple
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> lighting simple
> lighting full
> lighting soft
> lighting full
> lighting flat
> lighting flat
> graphics silhouettes false
> lighting simple
> select ::name="NAG"
1058 atoms, 1062 bonds, 58 residues, 3 models selected
> show sel target ab
> save "/Users/jingliu/OneDrive - GSK/Documents/CMV-
> related/CMV/gB-4H9modeling/gB-mutants-4H9binding.cxs"
——— End of log from Wed Feb 9 13:51:56 2022 ———
opened ChimeraX session
> color byattribute seq_conservation
64501 atoms, 5698 residues, 1 surfaces, atom seq_conservation range -4.36 to
0.439
> select ::name="NAG"
1058 atoms, 1062 bonds, 58 residues, 3 models selected
> hide sel target a
> color byattribute seq_conservation range -3, 3
64501 atoms, 5698 residues, 1 surfaces, atom seq_conservation range -4.36 to
0.439
> color byattribute seq_conservation range -2, 2
64501 atoms, 5698 residues, 1 surfaces, atom seq_conservation range -4.36 to
0.439
> color byattribute seq_conservation range -21.5 1.5
Invalid "range" argument: Need exactly 2 ','-separated numbers
> color byattribute seq_conservation range -1.5, 1.5
64501 atoms, 5698 residues, 1 surfaces, atom seq_conservation range -4.36 to
0.439
> color byattribute seq_conservation range -4, 1
64501 atoms, 5698 residues, 1 surfaces, atom seq_conservation range -4.36 to
0.439
> surface
> color fromatoms
> surface hidePatches sel
> select #2/D
998 atoms, 1020 bonds, 131 residues, 1 model selected
> surface hidePatches (#!2 & sel)
> select #2/E
796 atoms, 813 bonds, 110 residues, 1 model selected
> surface hidePatches (#!2 & sel)
> select #2/F
998 atoms, 1020 bonds, 131 residues, 1 model selected
> surface hidePatches (#!2 & sel)
> select #2/G
796 atoms, 813 bonds, 110 residues, 1 model selected
> surface hidePatches (#!2 & sel)
> select #2/I
796 atoms, 813 bonds, 110 residues, 1 model selected
> surface hidePatches (#!2 & sel)
> select #3/L
784 atoms, 805 bonds, 104 residues, 1 model selected
> surface hidePatches (#!3 & sel)
> select #2/H#3/H
1906 atoms, 1955 bonds, 1 pseudobond, 244 residues, 3 models selected
> surface hidePatches (#!2-3 & sel)
> select #1/T
1590 atoms, 1611 bonds, 112 residues, 1 model selected
> surface hidePatches (#!1 & sel)
> select #1/U
1882 atoms, 1910 bonds, 123 residues, 1 model selected
> surface hidePatches (#!1 & sel)
> select #1/X
1882 atoms, 1910 bonds, 123 residues, 1 model selected
> surface hidePatches (#!1 & sel)
> select #1/Y
1590 atoms, 1611 bonds, 112 residues, 1 model selected
> surface hidePatches (#!1 & sel)
> select #1/Y
1590 atoms, 1611 bonds, 112 residues, 1 model selected
> surface hidePatches (#!1 & sel)
> select #1/W
1590 atoms, 1611 bonds, 112 residues, 1 model selected
> surface hidePatches (#!1 & sel)
> select #1/V
1882 atoms, 1910 bonds, 123 residues, 1 model selected
> surface hidePatches (#!1 & sel)
> color byattribute seq_conservation palatte red:white:blue
Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword
> color fromatoms
> color surface byattr seq_conservation palette red-white-blue
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color byattribute seq_conservation palette red:white:blue
64501 atoms, 5698 residues, 21 surfaces, atom seq_conservation range -4.36 to
0.439
> select #1/A
9220 atoms, 9334 bonds, 2 pseudobonds, 572 residues, 2 models selected
> surface hidePatches (#!1 & sel)
[Repeated 1 time(s)]
> select #1/B
9317 atoms, 9432 bonds, 2 pseudobonds, 577 residues, 2 models selected
> cartoon hide (#!1 & sel)
> select clear
> select #1/C
9399 atoms, 9515 bonds, 2 pseudobonds, 583 residues, 2 models selected
> cartoon hide (#!1 & sel)
> select #1/A
9220 atoms, 9334 bonds, 2 pseudobonds, 572 residues, 2 models selected
> cartoon hide (#!1 & sel)
> select clear
> save "/Users/jl209164/OneDrive - GSK/Documents/CMV-
> related/CMV/gB-4H9-paper/gB-4H9-seq-conservationFeb24.cxs"
——— End of log from Thu Feb 24 15:44:07 2022 ———
opened ChimeraX session
> color byattribute attr seq_conservation
Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword
> select 7kdd chain A
Expected an objects specifier or a keyword
> select 7kdd
Expected an objects specifier or a keyword
> select select #2
Expected an objects specifier or a keyword
> select #2
19741 atoms, 20211 bonds, 9 pseudobonds, 2467 residues, 3 models selected
> color byattribute seq_conservation
64501 atoms, 5698 residues, 21 surfaces, atom seq_conservation range -4.36 to
0.439
> open 7kdp
7kdp title:
HCMV prefusion gB in complex with fusion inhibitor WAY-174865 [more info...]
Chain information for 7kdp #4
---
Chain | Description | UniProt
A B C | Envelope glycoprotein B | GB_HCMVT
Non-standard residues in 7kdp #4
---
CA — calcium ion
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
WCY —
N-{4-[({(1S)-1-[3,5-bis(trifluoromethyl)phenyl]ethyl}carbamothioyl)amino]phenyl}-1,3-thiazole-4-carboxamide
Associated 7kdp chain A to tr|A0A0G2TK23|A0A0G2TK23_HCMV with 0 mismatches
Associated 7kdp chain B to tr|A0A0G2TK23|A0A0G2TK23_HCMV with 0 mismatches
Associated 7kdp chain C to tr|A0A0G2TK23|A0A0G2TK23_HCMV with 0 mismatches
> select #4
15844 atoms, 16233 bonds, 3 pseudobonds, 1948 residues, 2 models selected
> color byattribute seq_conservation
80345 atoms, 7646 residues, 21 surfaces, atom seq_conservation range -4.36 to
0.439
> hide #!3 models
> hide #!2 models
> hide #!1 models
> surface (#!4 & sel)
> color byattribute seq_conservation
80345 atoms, 7646 residues, 24 surfaces, atom seq_conservation range -4.36 to
0.439
> hide (#!4 & sel) target a
> save "/Users/jl209164/OneDrive - GSK/Documents/CMV-related/gB-
> sequence20220602.aln"
> color byattribute seq_conservation palette blue:red -3.69, 0.439
Expected a keyword
> color byattribute seq_conservation palette blue:red range -3.69, 0.439
80345 atoms, 7646 residues, 24 surfaces, atom seq_conservation range -4.36 to
0.439
> color byattribute seq_conservation palette red:blue range -3.69, 0.439
80345 atoms, 7646 residues, 24 surfaces, atom seq_conservation range -4.36 to
0.439
> color byattribute seq_conservation palette red:blue range
Missing "range" keyword's argument
> color byattribute seq_conservation palette red:blue
80345 atoms, 7646 residues, 24 surfaces, atom seq_conservation range -4.36 to
0.439
> color byattribute seq_conservation palette red:white:blue
80345 atoms, 7646 residues, 24 surfaces, atom seq_conservation range -4.36 to
0.439
> color byattribute seq_conservation palette red:white:blue range -3.69, 0.439
80345 atoms, 7646 residues, 24 surfaces, atom seq_conservation range -4.36 to
0.439
> select clear
> show #!3 models
> hide #!4 models
> show #!2 models
> hide #!3 models
> show #!1 models
> hide #!2 models
> show #!4 models
> hide #!1 models
> show #!3 models
> show #!2 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!1 models
> show #!4 models
> hide #!1 models
> hide #* target a
> show #4 target ab
> select ::name="NAG"
1478 atoms, 1482 bonds, 88 residues, 4 models selected
> show (#!4 & sel) target ab
> select clear
> surface hidePatches #4
> lighting soft
> surface #4
> lighting full
> lighting soft
> color byattribute seq_conservation palette red:white:blue range
Missing "range" keyword's argument
> color byattribute seq_conservation palette red:white:blue
80345 atoms, 7646 residues, 24 surfaces, atom seq_conservation range -4.36 to
0.439
> ui tool show "Color Key"
> ui mousemode right "color key"
> key blue-white-red :min : :
> key blue-white-red :min : :v
> key blue-white-red :min : :va
> key blue-white-red :min : :var
> key blue-white-red :min : :vari
> key blue-white-red :min : :varia
> key blue-white-red :min : :variab
> key blue-white-red :min : :variabl
> key blue-white-red :min : :variable
> key blue-white-red :min : ":variable "
> key blue-white-red : : ":variable "
> key blue-white-red :c : ":variable "
> key blue-white-red :co : ":variable "
> key blue-white-red :con : ":variable "
> key blue-white-red :cons : ":variable "
> key blue-white-red :conse : ":variable "
> key blue-white-red :conser : ":variable "
> key blue-white-red :conserv : ":variable "
> key blue-white-red :conserva : ":variable "
> key blue-white-red :conservat : ":variable "
> key blue-white-red :conservati : ":variable "
> key blue-white-red :conservatio : ":variable "
> key blue-white-red :conservation : ":variable "
> key blue-white-red :conserv : ":variable "
> key blue-white-red :conserve : ":variable "
> key blue-white-red :conserved : ":variable "
> key blue-white-red :conserved : :varia
> key blue-white-red :conserved : :vari
> key blue-white-red :conserved : :varia
> key blue-white-red :conserved : :variab
> key blue-white-red :conserved : :variabl
> key blue-white-red :conserved : :variable
> key blue-white-red :conserved : :variabled
> key blue-white-red :conserved : ":variabled "
> key blue-white-red :conserved : :variabled
> key blue-white-red :conserved : :variable
> key blue-white-red :conserved : :variabl
> key blue-white-red :conserved : :variab
> key blue-white-red :conserved : :varia
> key blue-white-red :conserved : :vari
> key blue-white-red :conserved : :varie
> key blue-white-red :conserved : :varied
> key blue-white-red :conserved : ":varied "
> key blue-white-red :conserved : :varied
> key blue-white-red :conserved : :varie
> key blue-white-red :conserved : :vari
> key blue-white-red :conserved : :var
> key blue-white-red :conserved : :va
> key blue-white-red :conserved : :v
> key blue-white-red :conserved : :
> color byattribute seq_conservation palette red:white:blue range -4, 2
80345 atoms, 7646 residues, 24 surfaces, atom seq_conservation range -4.36 to
0.439
> color byattribute seq_conservation palette red:white:blue range -4, 4
80345 atoms, 7646 residues, 24 surfaces, atom seq_conservation range -4.36 to
0.439
> color byattribute seq_conservation palette red:white:blue range -4, 1
80345 atoms, 7646 residues, 24 surfaces, atom seq_conservation range -4.36 to
0.439
> color byattribute seq_conservation palette blue:white:white range -4, 1
80345 atoms, 7646 residues, 24 surfaces, atom seq_conservation range -4.36 to
0.439
> color byattribute seq_conservation palette blue:white:white range -4, 0.5
80345 atoms, 7646 residues, 24 surfaces, atom seq_conservation range -4.36 to
0.439
> key blue-white-red : : :
> key blue-white-red :v : :
> key blue-white-red :va : :
> key blue-white-red :var : :
> key blue-white-red :vari : :
> key blue-white-red :varib : :
> key blue-white-red :varibl : :
> key blue-white-red :varible : :
> key blue-white-red ":varible " : :
> key blue-white-red ":varible 0" : :
> key blue-white-red ":varible " : :
> key blue-white-red ":varible -" : :
> key blue-white-red ":varible -4" : :
> key blue-white-red ":varible -4" : :C
> key blue-white-red ":varible -4" : :Co
> key blue-white-red ":varible -4" : :Con
> key blue-white-red ":varible -4" : :Co
> key blue-white-red ":varible -4" : :C
> key blue-white-red ":varible -4" : :
> key blue-white-red ":varible -4" : :o
> key blue-white-red ":varible -4" : :on
> key blue-white-red ":varible -4" : :o
> key blue-white-red ":varible -4" : :
> key blue-white-red ":varible -4" : :c
> key blue-white-red ":varible -4" : :co
> key blue-white-red ":varible -4" : :con
> key blue-white-red ":varible -4" : :cons
> key blue-white-red ":varible -4" : :conss
> key blue-white-red ":varible -4" : :consse
> key blue-white-red ":varible -4" : :consser
> key blue-white-red ":varible -4" : :consserv
> key blue-white-red ":varible -4" : :consserve
> key blue-white-red ":varible -4" : :consserved
> key blue-white-red ":varible -4" : ":consserved "
> key blue-white-red ":varible -4" : ":consserved 1"
> key blue-white-red ":varible -4" : ":consserved "
> key blue-white-red ":varible -4" : ":consserved 0"
> color byattribute seq_conservation palette blue:white:white range -4, 0
80345 atoms, 7646 residues, 24 surfaces, atom seq_conservation range -4.36 to
0.439
> color byattribute seq_conservation palette blue:white:red range -4, 0
80345 atoms, 7646 residues, 24 surfaces, atom seq_conservation range -4.36 to
0.439
> color byattribute seq_conservation palette blue:white:red range -4, 4
80345 atoms, 7646 residues, 24 surfaces, atom seq_conservation range -4.36 to
0.439
> color byattribute seq_conservation palette blue:white:red range -4, 1
80345 atoms, 7646 residues, 24 surfaces, atom seq_conservation range -4.36 to
0.439
> key blue-white-red ":varible -4" : ":conserved 0"
> key blue-white-red ":varible -4" : ":conserved 0" white:
> key blue-white-red ":varible -4" : ":conserved 0"
> key red-white-blue ":conserved 0" : ":varible -4"
> key red-white-blue ":conserved " : ":varible -4"
> key red-white-blue ":conserved 1" : ":varible -4"
> key red-white-blue ":conserved 1" : ":varible -"
> key red-white-blue ":conserved 1" : ":varible -5"
> color byattribute seq_conservation palette blue:white:red range -5, 1
80345 atoms, 7646 residues, 24 surfaces, atom seq_conservation range -4.36 to
0.439
> color byattribute seq_conservation palette blue:white:red range -4, 1
80345 atoms, 7646 residues, 24 surfaces, atom seq_conservation range -4.36 to
0.439
> key red-white-blue ":conserved 1" : ":varible -"
> key red-white-blue ":conserved 1" : ":varible -4"
> color byattribute seq_conservation palette blue:white:red range -4, 0.5
80345 atoms, 7646 residues, 24 surfaces, atom seq_conservation range -4.36 to
0.439
> color byattribute seq_conservation palette blue:white:red range -4, 0.5
80345 atoms, 7646 residues, 24 surfaces, atom seq_conservation range -4.36 to
0.439
> key red-white-blue ":conserved 1" : ":varible -"
> key red-white-blue ":conserved 1" : ":varible "
> key red-white-blue ":conserved 1" : :varible
> key red-white-blue ":conserved " : :varible
> key red-white-blue :conserved : :varible
> save "/Users/jl209164/OneDrive - GSK/Documents/CMV-
> related/CMV/gB-4H9-paper/gB_conservartion.cxs"
> show #!3 models
> hide #!4 models
> show #!2 models
> open /Users/jl209164/Library/CloudStorage/OneDrive-GSK/Documents/CMV-
> related/CMV/gB-ITC63/Map/20220518/20220509/gB758_ITC63b_05262022.pdb
Chain information for gB758_ITC63b_05262022.pdb #6
---
Chain | Description
A B C | No description available
E H M | No description available
F L N | No description available
Associated gB758_ITC63b_05262022.pdb chain A to tr|A0A3G6XLA9|A0A3G6XLA9_HCMV
with 9 mismatches
Associated gB758_ITC63b_05262022.pdb chain B to tr|A0A3G6XLA9|A0A3G6XLA9_HCMV
with 9 mismatches
Associated gB758_ITC63b_05262022.pdb chain C to tr|A0A3G6XLA9|A0A3G6XLA9_HCMV
with 9 mismatches
> hide #2-3,5-6 target a
> cartoon #2-3,5-6
> surface #2-3,5-6
> color byattribute seq_conservation palette blue:white:red range -4, 0.5
129419 atoms, 10817 residues, 33 surfaces, atom seq_conservation range -4.36
to 0.439
> ui mousemode right translate
> hide #!2 models
> hide #5 models
> hide #!3 models
> select #2/H#3/H#6/H
5365 atoms, 5460 bonds, 1 pseudobond, 478 residues, 4 models selected
> cartoon hide (#!6 & sel)
> surface hidePatches (#!6 & sel)
> cartoon (#!6 & sel)
> select #3/L#6/L
3943 atoms, 4006 bonds, 317 residues, 2 models selected
> surface hidePatches (#!6 & sel)
> cartoon (#!6 & sel)
> select clear
> ui tool show "Color Actions"
> color thistle
[Repeated 1 time(s)]
> color byattribute seq_conservation palette blue:white:red range -4, 0.5
129419 atoms, 10817 residues, 33 surfaces, atom seq_conservation range -4.36
to 0.439
> color pale green
> color byattribute seq_conservation palette blue:white:red range -4, 0.5
129419 atoms, 10817 residues, 33 surfaces, atom seq_conservation range -4.36
to 0.439
> select #6/E
3459 atoms, 3505 bonds, 234 residues, 1 model selected
> surface hidePatches (#!6 & sel)
> cartoon hide (#!6 & sel)
> select #6/F
3159 atoms, 3201 bonds, 213 residues, 1 model selected
> cartoon hide (#!6 & sel)
> surface hidePatches (#!6 & sel)
> select #6/M
3459 atoms, 3505 bonds, 234 residues, 1 model selected
> surface hidePatches (#!6 & sel)
> cartoon hide (#!6 & sel)
> select #6/N
3159 atoms, 3201 bonds, 213 residues, 1 model selected
> cartoon hide (#!6 & sel)
> surface hidePatches (#!6 & sel)
> select #6/H
3459 atoms, 3505 bonds, 234 residues, 1 model selected
> color sel thistle
> select clear
> select #6/H
3459 atoms, 3505 bonds, 234 residues, 1 model selected
> color sel pale green
> select #6/L
3159 atoms, 3201 bonds, 213 residues, 1 model selected
> color sel thistle
> select clear
> color byattribute seq_conservation palette blue:white:red
129419 atoms, 10817 residues, 33 surfaces, atom seq_conservation range -4.36
to 0.439
> ui tool show "Color Key"
> ui mousemode right "color key"
> key red-white-blue :conserved : :varible
> key pos 0.628809,0.670439 size 0,0
> key pos 0.51302,0.639971 size 0.000221179,0
> key pos 0.664636,0.637714 size 0,0
> key red-white-blue :conserved : :varible
> key delete
> ui mousemode right translate
> ui tool show "Color Key"
> ui mousemode right "color key"
> key blue-white-red :min : :c
> key blue-white-red :min : :co
> key blue-white-red :min : :cos
> key blue-white-red :min : :cose
> key blue-white-red :min : :coser
> key blue-white-red :min : :coserv
> key blue-white-red :min : :coserve
> key blue-white-red :min : :coserved
> key blue-white-red :min : ":coserved "
> key blue-white-red :v : ":coserved "
> key blue-white-red :va : ":coserved "
> key blue-white-red :var : ":coserved "
> key blue-white-red :vari : ":coserved "
> key blue-white-red :varib : ":coserved "
> key blue-white-red :varibl : ":coserved "
> key blue-white-red :varible : ":coserved "
> key pos 0.69000,0.08000
> key pos 0.68000,0.08000
> key pos 0.67000,0.08000
> key pos 0.66000,0.08000
> key pos 0.65000,0.08000
> key pos 0.64000,0.08000
> key pos 0.63000,0.08000
> key pos 0.62000,0.08000
> key pos 0.61000,0.08000
> key pos 0.60000,0.08000
> key pos 0.59000,0.08000
> key pos 0.58000,0.08000
> key pos 0.57000,0.08000
> key pos 0.56000,0.08000
> key pos 0.55000,0.08000
> key pos 0.54000,0.08000
> key pos 0.53000,0.08000
> key pos 0.52000,0.08000
> key pos 0.51000,0.08000
> key pos 0.50000,0.08000
> key pos 0.49000,0.08000
> key pos 0.48000,0.08000
> key pos 0.47000,0.08000
> key pos 0.46000,0.08000
> key pos 0.45000,0.08000
> key pos 0.44000,0.08000
> key pos 0.44000,0.07000
> key pos 0.44000,0.06000
> key pos 0.44000,0.05000
> key pos 0.44000,0.06000
> key pos 0.44000,0.07000
> key pos 0.44000,0.08000
> key pos 0.44000,0.09000
> key pos 0.44000,0.10000
> key size 0.24000,0.05000
> key size 0.23000,0.05000
> key size 0.22000,0.05000
> key size 0.21000,0.05000
> key size 0.20000,0.05000
> key size 0.19000,0.05000
> key size 0.18000,0.05000
> key size 0.17000,0.05000
> key size 0.16000,0.05000
> key size 0.15000,0.05000
> key size 0.14000,0.05000
> key size 0.14000,0.04000
> key size 0.14000,0.03000
> key size 0.14000,0.02000
> key border false
> key blue-white-red :varible : ":coserved ("
> key blue-white-red :varible : ":coserved (0"
> key blue-white-red :varible : ":coserved ("
> key blue-white-red :varible : ":coserved "
> key blue-white-red :varible : :coserved
> key blue-white-red :varible : :coserved-
> key blue-white-red :varible : :coserved-0
> key blue-white-red :varible : :coserved-0.
> key blue-white-red :varible : :coserved-0.4
> key blue-white-red :varible : :coserved-0.43
> key blue-white-red :varible : :coserved-0.439
> key blue-white-red :varible- : :coserved-0.439
> key blue-white-red :varible : :coserved-0.439
> key blue-white-red ":varible " : :coserved-0.439
> key blue-white-red ":varible " : :coserved0.439
> key blue-white-red ":varible " : ":coserved0.439 "
> key blue-white-red ":varible " : ":coserved 0.439 "
> key blue-white-red ":varible " : ":coserved "
> key blue-white-red ":varible " : :coserved
> key pos 0.44000,0.09000
> key pos 0.44000,0.10000
> key pos 0.45000,0.10000
> key pos 0.46000,0.10000
> key pos 0.47000,0.10000
> key pos 0.48000,0.10000
> key pos 0.49000,0.10000
> key size 0.15000,0.02000
> key size 0.16000,0.02000
> key size 0.17000,0.02000
> key size 0.18000,0.02000
> key size 0.19000,0.02000
> key size 0.20000,0.02000
> key size 0.19000,0.02000
> key size 0.18000,0.02000
> key size 0.17000,0.02000
> key size 0.16000,0.02000
> key size 0.15000,0.02000
> key size 0.14000,0.02000
> key size 0.13000,0.02000
> key size 0.12000,0.02000
> key size 0.11000,0.02000
> key size 0.10000,0.02000
> key size 0.09000,0.02000
> key size 0.10000,0.02000
> key size 0.11000,0.02000
> key fontSize 20
> key blue-white-red ":varible " : :conserved
> save /Users/jl209164/Library/CloudStorage/OneDrive-GSK/Documents/CMV-
> related/CMV/gB-conservation_withallFabs_20220601.cxs
> ui mousemode right translate
> save "/Users/jl209164/OneDrive -
> GSK/Documents/IPTc&developmentPlan/GSK-R&Dday/2022/gB-
> ITC63_interface_conserved.tif" width 1042 height 789 supersample 3
> lighting soft
> ui tool show "Color Key"
> ui mousemode right "color key"
> key pos 0.49000,0.09000
> key pos 0.49000,0.08000
> key pos 0.49000,0.07000
> key pos 0.50000,0.07000
> key pos 0.51000,0.07000
> key pos 0.52000,0.07000
> key pos 0.53000,0.07000
> key pos 0.54000,0.07000
> key pos 0.55000,0.07000
> key pos 0.56000,0.07000
> key size 0.12000,0.02000
> key size 0.13000,0.02000
> key size 0.14000,0.02000
> key size 0.14000,0.03000
> key size 0.14000,0.04000
> key size 0.14000,0.05000
> key size 0.14000,0.04000
> key fontSize 24
> ui mousemode right translate
> save "/Users/jl209164/OneDrive -
> GSK/Documents/IPTc&developmentPlan/GSK-R&Dday/2022/gB-
> ITC63_interface_conserved_zoom.tif" width 1042 height 789 supersample 3
> hide #!6 models
> show #!4 models
> save "/Users/jl209164/OneDrive -
> GSK/Documents/IPTc&developmentPlan/GSK-R&Dday/2022/prefusiongB_surface_conservation.tif"
> width 1042 height 789 supersample 3
> hide #!4 models
> show #!3 models
> select #3/H
908 atoms, 935 bonds, 1 pseudobond, 113 residues, 2 models selected
> surface hidePatches (#!3 & sel)
> color sel light goldenrod yellow
[Repeated 1 time(s)]
> color sel light pink
> select #3/L
784 atoms, 805 bonds, 104 residues, 1 model selected
> color sel plum
> surface hidePatches (#!3 & sel)
> color sel lavender
> color sel light cyan
> color sel plum
> color sel light green
> color sel powder blue
> color sel pale turquoise
> select #3/H
908 atoms, 935 bonds, 1 pseudobond, 113 residues, 2 models selected
> color sel light green
> select clear
> save "/Users/jl209164/OneDrive -
> GSK/Documents/IPTc&developmentPlan/GSK-R&Dday/2022/gB-1G2_interface_conserved_zoom.tif"
> width 1042 height 789 supersample 3
> save "/Users/jl209164/OneDrive -
> GSK/Documents/IPTc&developmentPlan/GSK-R&Dday/2022/gB-1G2_interface_conserved.tif"
> width 1042 height 789 supersample 3
> hide #!3 models
> show #!2 models
> select #2/G
796 atoms, 813 bonds, 110 residues, 1 model selected
> show #!1 models
> hide #!2 models
> select #1/C
9399 atoms, 9515 bonds, 2 pseudobonds, 583 residues, 2 models selected
> surface (#!1 & sel)
> select #1/B
9317 atoms, 9432 bonds, 2 pseudobonds, 577 residues, 2 models selected
> surface (#!1 & sel)
> select #1/A
9220 atoms, 9334 bonds, 2 pseudobonds, 572 residues, 2 models selected
> surface (#!1 & sel)
> select clear
> select #1/T
1590 atoms, 1611 bonds, 112 residues, 1 model selected
> color sel thistle
> select #1/U
1882 atoms, 1910 bonds, 123 residues, 1 model selected
> color sel pale green
> select clear
> save "/Users/jl209164/OneDrive -
> GSK/Documents/IPTc&developmentPlan/GSK-R&Dday/2022/gB-4H9_interface_conservation.tif"
> width 1042 height 789 supersample 3
> save "/Users/jl209164/OneDrive -
> GSK/Documents/IPTc&developmentPlan/GSK-R&Dday/2022/gB-4H9_interface_conservation_zoom.tif"
> width 1042 height 789 supersample 3
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #2/I
796 atoms, 813 bonds, 110 residues, 1 model selected
> surface hidePatches (#!2 & sel)
> cartoon hide (#!2 & sel)
> select #2/E
796 atoms, 813 bonds, 110 residues, 1 model selected
> select #2/G
796 atoms, 813 bonds, 110 residues, 1 model selected
> cartoon hide (#!2 & sel)
> surface hidePatches (#!2 & sel)
> select #2/D
998 atoms, 1020 bonds, 131 residues, 1 model selected
> surface hidePatches (#!2 & sel)
> select #2/E
796 atoms, 813 bonds, 110 residues, 1 model selected
> surface hidePatches (#!2 & sel)
> color sel sky blue
> color sel light sky blue
> color sel light coral
> color sel rosy brown
> color sel orchid
> color sel deep pink
> color sel rebecca purple
> color sel slate blue
> color sel dark olive green
> color sel cyan
> select #2/F
998 atoms, 1020 bonds, 131 residues, 1 model selected
> surface hidePatches (#!2 & sel)
> cartoon hide (#!2 & sel)
> select #2/H
998 atoms, 1020 bonds, 131 residues, 1 model selected
> cartoon hide (#!2 & sel)
> surface hidePatches (#!2 & sel)
> color byattribute seq_conservation palette blue:white:red
129419 atoms, 10817 residues, 33 surfaces, atom seq_conservation range -4.36
to 0.439
> set bgColor white
> set bgColor black
[Repeated 1 time(s)]
> set bgColor white
> lighting soft
> lighting full
> lighting soft
> ui tool show "Selection Inspector"
> save "/Users/jl209164/OneDrive -
> GSK/Documents/IPTc&developmentPlan/GSK-R&Dday/2022/gB-
> SM-5_interface_conserved.tif" width 1042 height 789 supersample 3
> save "/Users/jl209164/OneDrive -
> GSK/Documents/IPTc&developmentPlan/GSK-R&Dday/2022/gB-
> SM-5_interface_conserved_zoom.tif" width 1042 height 789 supersample 3
> save "/Users/jl209164/OneDrive -
> GSK/Documents/IPTc&developmentPlan/GSK-R&Dday/2022/gB-
> surface_sequenceconservation.cxs"
——— End of log from Wed Jun 1 11:14:26 2022 ———
opened ChimeraX session
> show #!1 models
> hide #!2 models
> surface hidePatches #1,7
> cartoon #1,7
> surface #1,7
> select #1/T
1590 atoms, 1611 bonds, 112 residues, 1 model selected
> ui tool show "Color Actions"
> color sel medium orchid
> surface hidePatches (#!1 & sel)
> select #1/U
1882 atoms, 1910 bonds, 123 residues, 1 model selected
> color sel cyan
> surface hidePatches (#!1 & sel)
> select #1/V
1882 atoms, 1910 bonds, 123 residues, 1 model selected
> color sel cyan
> surface hidePatches (#!1 & sel)
> cartoon hide (#!1 & sel)
> select #1/W
1590 atoms, 1611 bonds, 112 residues, 1 model selected
> color sel medium orchid
> surface hidePatches (#!1 & sel)
> cartoon hide (#!1 & sel)
> select #1/X
1882 atoms, 1910 bonds, 123 residues, 1 model selected
> color sel cyan
> surface hidePatches (#!1 & sel)
> select #1/Y
1590 atoms, 1611 bonds, 112 residues, 1 model selected
> color sel medium orchid
> surface hidePatches (#!1 & sel)
> select clear
> ui tool show "Color Key"
> ui mousemode right "color key"
> key pos 0.55000,0.07000
> key pos 0.54000,0.07000
> key pos 0.54000,0.06000
> key pos 0.54000,0.05000
> ui mousemode right translate
> select #1/W
1590 atoms, 1611 bonds, 112 residues, 1 model selected
> cartoon (#!1 & sel)
> select #1/W
1590 atoms, 1611 bonds, 112 residues, 1 model selected
> cartoon (#!1 & sel)
> save "/Users/jl209164/OneDrive -
> GSK/Documents/IPTc&developmentPlan/GSK-R&Dday/2022/gB-4H9_interface_conservation.tif"
> width 842 height 792 supersample 3
> ui tool show "Color Key"
> ui mousemode right "color key"
> key pos 0.53000,0.05000
> key pos 0.52000,0.05000
> key pos 0.52000,0.04000
> key pos 0.52000,0.03000
> key pos 0.52000,0.02000
> key pos 0.52000,0.01000
> key pos 0.52000,0.00000
> key pos 0.51000,0.00000
> ui mousemode right translate
> save "/Users/jl209164/OneDrive -
> GSK/Documents/IPTc&developmentPlan/GSK-R&Dday/2022/gB-4H9_interface_conservation_zoom.tif"
> width 842 height 792 supersample 3
> save "/Users/jl209164/OneDrive -
> GSK/Documents/IPTc&developmentPlan/GSK-R&Dday/2022/gB-4H9-interfaceconservation/gB-
> surface_0602.cxs"
——— End of log from Thu Jun 2 10:58:00 2022 ———
opened ChimeraX session
> show #!6 models
> hide #!1 models
> show #!1 models
> ui tool show Matchmaker
> matchmaker #!1 to #6
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker gB758_ITC63b_05262022.pdb, chain A (#6) with
gB-4H9_rmC_Jan312022_real_space_refined_007.pdb, chain B (#1), sequence
alignment score = 2681.5
RMSD between 422 pruned atom pairs is 1.238 angstroms; (across all 568 pairs:
2.587)
> close session
> open /Users/jl209164/Library/CloudStorage/OneDrive-GSK/Documents/CMV-
> related/CMV/gB-
> ITC63/Map/20220518/20220509/Postprocess059/postprocess_masked.mrc format mrc
Opened postprocess_masked.mrc as #1, grid size 416,416,416, pixel 0.88, shown
at level 0.00624, step 2, values float32
> volume #1 level 0.009074
> volume #1 step 1
> volume #1 level 0.01476
> open /Users/jl209164/Library/CloudStorage/OneDrive-GSK/Documents/CMV-
> related/CMV/gB-
> ITC63/Map/20220518/20220509/Postprocess059/postprocess_masked.mrc
Opened postprocess_masked.mrc as #2, grid size 416,416,416, pixel 0.88, shown
at level 0.00624, step 2, values float32
> open /Users/jl209164/Library/CloudStorage/OneDrive-GSK/Documents/CMV-
> related/CMV/gB-ITC63/Map/20220518/20220509/gB758_ITC63b_05262022.pdb
Chain information for gB758_ITC63b_05262022.pdb #3
---
Chain | Description
A B C | No description available
E H M | No description available
F L N | No description available
> volume #2 level 0.01397
> volume #2 step 1
> close #2
> hide #3 models
> volume #1 level 0.01394
> show #3 models
> select /A
9740 atoms, 9854 bonds, 610 residues, 1 model selected
> color sel light gray
> select /B
9740 atoms, 9854 bonds, 610 residues, 1 model selected
> color sel dim gray
> select /C
9740 atoms, 9854 bonds, 610 residues, 1 model selected
> color sel blue
> select /E
3459 atoms, 3505 bonds, 234 residues, 1 model selected
> select /H
3459 atoms, 3505 bonds, 234 residues, 1 model selected
> ui tool show "Color Actions"
> color sel fire brick
> select /E
3459 atoms, 3505 bonds, 234 residues, 1 model selected
> color sel fire brick
> color sel indian red
> color sel fire brick
> select /M
3459 atoms, 3505 bonds, 234 residues, 1 model selected
> color sel fire brick
> select /L
3159 atoms, 3201 bonds, 213 residues, 1 model selected
> color sel hot pink
> select /N
3159 atoms, 3201 bonds, 213 residues, 1 model selected
> color sel hot pink
> select /F
3159 atoms, 3201 bonds, 213 residues, 1 model selected
> color sel hot pink
> ui tool show "Color Zone"
> color zone #1 near #3 distance 6.08
> hide #3 models
> volume #1 level 0.01568
> lighting soft
> lighting full
> save /Users/jl209164/Documents/gB_ITC63_202205.tif models #1 format
> imagejtiff
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/toolbar/tool.py", line 165, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 381, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1284, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/__init__.py", line 37, in run_provider
providers.run_provider(session, name)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/providers.py", line 45, in run_provider
what(session)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/providers.py", line 27, in _file_save
show_save_file_dialog(session)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
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/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
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/save_command/cmd.py", line 89, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/__init__.py", line 185, in save
save_map(session, path, _name, **kw)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 3972, in save_map
save_grid_data(grids, path, session, format_name, options)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/fileformats.py", line 314, in save_grid_data
ff.save_func(garg, tpath, options = options, progress = p)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/imagestack/imagej_write.py", line 19, in
write_imagej_tiff
_write_3d_tiff(grid_data, path)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/imagestack/imagej_write.py", line 29, in
_write_3d_tiff
imwrite(path, array_zcyx, imagej=True, resolution=(1/xstep, 1/ystep),
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/tifffile/tifffile.py", line 856, in imwrite
result = tif.write(data, shape, dtype, **kwargs)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/tifffile/tifffile.py", line 1640, in write
ijshape = imagej_shape(
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/tifffile/tifffile.py", line 14066, in imagej_shape
raise ValueError('ImageJ hyperstack shape and axes do not match')
ValueError: ImageJ hyperstack shape and axes do not match
ValueError: ImageJ hyperstack shape and axes do not match
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/tifffile/tifffile.py", line 14066, in imagej_shape
raise ValueError('ImageJ hyperstack shape and axes do not match')
See log for complete Python traceback.
> save /Users/jl209164/Desktop/image1.png supersample 3
> select /C
9740 atoms, 9854 bonds, 610 residues, 1 model selected
> ui tool show "Color Actions"
> color sel cornflower blue
> color sel deep sky blue
> color sel cornflower blue
> color zone #1 near #3 distance 6.08
> save /Users/jl209164/Desktop/image2.png supersample 3
> lighting soft
> save /Users/jl209164/Desktop/image1.png supersample 3
> save "/Users/jl209164/OneDrive - GSK/Documents/CMV-related/CMV/gB-
> ITC63/Map/20220518/20220509/gB-ITC63b.cxs"
> turn x 90
> turn x 270
> turn xy270
Expected an axis vector or a keyword
> turn y270
Expected an axis vector or a keyword
> turn y90
Expected an axis vector or a keyword
> turn y 90
> turn y 270
> turn yx270
Expected an axis vector or a keyword
> turn x 90
> turn x 180
> save /Users/jl209164/Desktop/image2.png supersample 3
> save "/Users/jl209164/OneDrive - GSK/Documents/CMV-related/CMV/gB-
> ITC63/Map/20220518/20220509/gB-ITC63b_density_top.tif" models #1 format
> imagejtiff
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/toolbar/tool.py", line 165, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 381, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1284, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/__init__.py", line 37, in run_provider
providers.run_provider(session, name)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/providers.py", line 45, in run_provider
what(session)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/providers.py", line 27, in _file_save
show_save_file_dialog(session)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
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/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
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/save_command/cmd.py", line 89, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/__init__.py", line 185, in save
save_map(session, path, _name, **kw)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 3972, in save_map
save_grid_data(grids, path, session, format_name, options)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/fileformats.py", line 314, in save_grid_data
ff.save_func(garg, tpath, options = options, progress = p)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/imagestack/imagej_write.py", line 19, in
write_imagej_tiff
_write_3d_tiff(grid_data, path)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/imagestack/imagej_write.py", line 29, in
_write_3d_tiff
imwrite(path, array_zcyx, imagej=True, resolution=(1/xstep, 1/ystep),
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/tifffile/tifffile.py", line 856, in imwrite
result = tif.write(data, shape, dtype, **kwargs)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/tifffile/tifffile.py", line 1640, in write
ijshape = imagej_shape(
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/tifffile/tifffile.py", line 14066, in imagej_shape
raise ValueError('ImageJ hyperstack shape and axes do not match')
ValueError: ImageJ hyperstack shape and axes do not match
ValueError: ImageJ hyperstack shape and axes do not match
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/tifffile/tifffile.py", line 14066, in imagej_shape
raise ValueError('ImageJ hyperstack shape and axes do not match')
See log for complete Python traceback.
> save "/Users/jl209164/OneDrive - GSK/Documents/CMV-related/CMV/gB-
> ITC63/Map/20220518/20220509/gB-ITC63b.cxs"
> open /Users/jl209164/Library/CloudStorage/OneDrive-GSK/Documents/CMV-
> related/CMV/gB-4H9modeling/gB-4H9_Feb08-2022.pdb
Chain information for gB-4H9_Feb08-2022.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
T W Y | No description available
U V X | No description available
> open /Users/jl209164/Library/CloudStorage/OneDrive-GSK/Documents/CMV-
> related/CMV/gB-4H9modeling/gB-4H9_Feb08-2022.pdb
Chain information for gB-4H9_Feb08-2022.pdb #4
---
Chain | Description
A | No description available
B | No description available
C | No description available
T W Y | No description available
U V X | No description available
> close #2
> close #4
> close session
> open /Users/jl209164/Library/CloudStorage/OneDrive-GSK/Documents/CMV-
> related/CMV/gB-4H9modeling/gB-4H9_Feb08-2022.pdb format pdb
Chain information for gB-4H9_Feb08-2022.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
T W Y | No description available
U V X | No description available
> select #1
47612 atoms, 48217 bonds, 9 pseudobonds, 3067 residues, 2 models selected
> hide (#!1 & sel) target a
> cartoon (#!1 & sel)
> select ::name="NAG"
498 atoms, 501 bonds, 18 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> select #:NAG817
Expected an objects specifier or a keyword
> select ::name="NAG"
498 atoms, 501 bonds, 18 residues, 1 model selected
> show sel target ab
> select clear
> select :NAG817
Nothing selected
> open /Users/jl209164/Library/CloudStorage/OneDrive-GSK/Documents/CMV-
> related/CMV/gB-4H9modeling/gB759-4H9.mrc
Opened gB759-4H9.mrc as #2, grid size 512,512,512, pixel 0.66, shown at level
2.53, step 2, values float32
> volume #2 step 1
> volume #2 level 5.372
> volume #2 color #b2ffff8e
> volume #2 color #b2ffff5f
> volume #2 color #b2ffff5e
> volume #2 color #f8f6fe5e
[Repeated 2 time(s)]
> lighting soft
> volume #2 color #bcbbc15e
> volume #2 color #cccad15e
> volume #2 color #b7b6bb5e
[Repeated 1 time(s)]
> volume #2 level 6.319
> volume style mesh
> volume style image
> volume style surface
> lighting flat
> select /V:53
20 atoms, 20 bonds, 1 residue, 1 model selected
> hide #* target a
> show sel target ab
> hide sel target a
> show (sel-residues & sidechain) target ab
> graphics silhouettes false
> lighting flat
[Repeated 1 time(s)]
> lighting full
> lighting shadows false
> lighting flat
> style sel stick
Changed 20 atom styles
> select ::name="NAG"
498 atoms, 501 bonds, 18 residues, 1 model selected
> show sel target ab
> lighting soft
[Repeated 1 time(s)]
> lighting flat
> select /V:31
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> show sel target ab
> select /V:30
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel target ab
> style sel stick
Changed 11 atom styles
> select /V:54
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel target ab
> style sel stick
Changed 14 atom styles
> graphics silhouettes false
> lighting shadows true intensity 0.5
> graphics silhouettes true
> lighting flat
[Repeated 1 time(s)]
> select /V
3367 atoms, 3415 bonds, 226 residues, 1 model selected
> color sel cyan
> select /W
3191 atoms, 3229 bonds, 1 pseudobond, 219 residues, 2 models selected
> cartoon hide (#!1 & sel)
> select /A
9220 atoms, 9334 bonds, 2 pseudobonds, 572 residues, 2 models selected
> color (#!1 & sel) blue
> select /A:817@C4
1 atom, 1 residue, 1 model selected
> hide #!2 models
> select /A:818@C2
1 atom, 1 residue, 1 model selected
> select ::name="NAG"
498 atoms, 501 bonds, 18 residues, 1 model selected
> color sel byelement
> select /A:208
13 atoms, 12 bonds, 1 residue, 1 model selected
> style sel stick
Changed 13 atom styles
> show sel target ab
> show #!2 models
> lighting flat
[Repeated 1 time(s)]
> lighting full
> lighting flat
> select /V:53@CB
1 atom, 1 residue, 1 model selected
> color sel byelement
> hide #!1 models
> show #!1 models
> hide #!2 models
> select /V:53@CD1
1 atom, 1 residue, 1 model selected
> select /V:53@CD1
1 atom, 1 residue, 1 model selected
> select /V:31
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel byelement
> select /V:53
20 atoms, 20 bonds, 1 residue, 1 model selected
> color sel byelement
[Repeated 1 time(s)]
> select /V:54@CA
1 atom, 1 residue, 1 model selected
> color sel byelement
> select clear
> select /V:54
14 atoms, 13 bonds, 1 residue, 1 model selected
> color sel byelement
> select /V:30
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel byelement
> ui tool show "Color Actions"
> show #!2 models
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting flat
> ui tool show "Side View"
> view sel
[Repeated 1 time(s)]
> view
> select /V:53
20 atoms, 20 bonds, 1 residue, 1 model selected
> select /V:31
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /V:54@CA
1 atom, 1 residue, 1 model selected
> select /A:817@C5
1 atom, 1 residue, 1 model selected
> select /A:208@CG
1 atom, 1 residue, 1 model selected
> select /A:818@C1
1 atom, 1 residue, 1 model selected
> select /A:818@C3
1 atom, 1 residue, 1 model selected
> select /A:818@C4
1 atom, 1 residue, 1 model selected
> select /A:818@C5
1 atom, 1 residue, 1 model selected
> select /A:818@C6
1 atom, 1 residue, 1 model selected
> select /A:818@O5
1 atom, 1 residue, 1 model selected
> select add /V:53
21 atoms, 20 bonds, 2 residues, 1 model selected
> select add /V:30
32 atoms, 30 bonds, 3 residues, 1 model selected
> select add /V:31
43 atoms, 40 bonds, 4 residues, 1 model selected
> select add /V:54@CA
44 atoms, 40 bonds, 5 residues, 1 model selected
> select add /A:208@CG
45 atoms, 42 bonds, 6 residues, 1 model selected
> select add /A:817@C6
46 atoms, 42 bonds, 7 residues, 1 model selected
> select add /A:818@C4
47 atoms, 45 bonds, 7 residues, 1 model selected
> select add /A:818@C5
48 atoms, 45 bonds, 7 residues, 1 model selected
> select add /A:818@C6
49 atoms, 45 bonds, 7 residues, 1 model selected
> select add /A:817@C3
50 atoms, 46 bonds, 7 residues, 1 model selected
> select add /A:817@C2
51 atoms, 46 bonds, 7 residues, 1 model selected
> select add /A:817@H83
52 atoms, 47 bonds, 7 residues, 1 model selected
> view sel
> select clear
> save "/Users/jl209164/OneDrive - GSK/Documents/CMV-
> related/CMV/gB-4H9-paper/Figures/Figure2_4H9-gB-
> interface/gB-N208-Glycan.cxs"
> save "/Users/jl209164/OneDrive - GSK/Documents/CMV-
> related/CMV/gB-4H9-paper/Figures/Figure2_4H9-gB-
> interface/gB-N208-glycan.tif" models #2 format imagejtiff
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/toolbar/tool.py", line 165, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 381, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1284, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/__init__.py", line 37, in run_provider
providers.run_provider(session, name)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/providers.py", line 45, in run_provider
what(session)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/providers.py", line 27, in _file_save
show_save_file_dialog(session)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
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/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
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/save_command/cmd.py", line 89, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/__init__.py", line 185, in save
save_map(session, path, _name, **kw)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 3972, in save_map
save_grid_data(grids, path, session, format_name, options)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/fileformats.py", line 314, in save_grid_data
ff.save_func(garg, tpath, options = options, progress = p)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/imagestack/imagej_write.py", line 19, in
write_imagej_tiff
_write_3d_tiff(grid_data, path)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/imagestack/imagej_write.py", line 29, in
_write_3d_tiff
imwrite(path, array_zcyx, imagej=True, resolution=(1/xstep, 1/ystep),
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/tifffile/tifffile.py", line 856, in imwrite
result = tif.write(data, shape, dtype, **kwargs)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/tifffile/tifffile.py", line 1640, in write
ijshape = imagej_shape(
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/tifffile/tifffile.py", line 14066, in imagej_shape
raise ValueError('ImageJ hyperstack shape and axes do not match')
ValueError: ImageJ hyperstack shape and axes do not match
ValueError: ImageJ hyperstack shape and axes do not match
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/tifffile/tifffile.py", line 14066, in imagej_shape
raise ValueError('ImageJ hyperstack shape and axes do not match')
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Max
OpenGL vendor: AppleHardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,2
Processor Name: Unknown
Processor Speed: 2.4 GHz
Number of Processors: 1
Total Number of Cores: 10
L2 Cache: 20 MB
Memory: 64 GB
Software:
System Software Overview:
System Version: macOS 12.4 (21F79)
Kernel Version: Darwin 21.5.0
Time since boot: 3 days 2:17
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 32
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
HP E231:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
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-Clipper: 0.17.0
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-ISOLDE: 1.3
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 (4)
comment:1 by , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Input/Output |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Save TIFF, not TIFF stack |
comment:2 by , 3 years ago
| Resolution: | → not a bug |
|---|---|
| Status: | accepted → closed |
follow-up: 3 comment:3 by , 3 years ago
Thanks, Eric. I see what I did wrong now. Have a great weekend!
Best,
Jing
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Friday, June 3, 2022 at 2:18 PM
To:
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>, Jing Liu <jing.16.liu@gsk.com>, pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #7021: Save TIFF, not TIFF stack
EXTERNAL
#7021: Save TIFF, not TIFF stack
------------------------------------+--------------------
Reporter: jing.16.liu@… | Owner: pett
Type: defect | Status: closed
Priority: normal | Milestone:
Component: Input/Output | Version:
Resolution: not a bug | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
------------------------------------+--------------------
Changes (by pett):
* status: accepted => closed
* resolution: => not a bug
Comment:
Hi Jing,
In order to save a TIFF image you have to select "TIFF image" as
the format, not "ImageJ TIFF map". The latter is for saving volumetric
data as a map consisting of stacked TIFF images.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
--
Ticket URL: <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7021*comment:2__;Iw!!AoaiBx6H!2XnQ4fdH-v0KgeSSVhvSEscee8titcSCZsGvsPiz5jYkjicrk5xQFeU45TyLabekbn_9d8M6JNpJ0OzJWBMt8lKbAlM-WbnZRQ$ >
ChimeraX <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/__;!!AoaiBx6H!2XnQ4fdH-v0KgeSSVhvSEscee8titcSCZsGvsPiz5jYkjicrk5xQFeU45TyLabekbn_9d8M6JNpJ0OzJWBMt8lKbAlM5JPjB_w$ >
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comment:4 by , 3 years ago
Saving as an ImageJ TIFF stack should have worked. That traceback resulted from a bug #5881 that was fixed 5 months ago (fixed in 1.4 release).
But it sounds like you just wanted a screen snapshot so command "save myfigure2.tif" is what you want without specifying the format at imagejtiff which is a specialized volume data format.
Note:
See TracTickets
for help on using tickets.
Hi Jing,
--Eric