That is correct. You would need to start ChimeraX with the --offscreen flag to be able to save images in nogui mode (offscreen implies nogui). And that only works with the Ubuntu and CentOS versions of ChimeraX. -- Greg On 1/14/2022 2:48 PM, Elaine Meng via Chimera-users wrote:
Hello, It isn't my area of expertise, but I don't think you can save images in nogui mode except with Linux OSMesa.
As for your other questions, which commands do certain things...
may you suggest some commands that I may introduce into my batch file to 1) delete all models from the multi-model pdb file with the exemption of the first model. 2) switch from cartoon to surface representation of the protein 3) visualize protein-ligand non-covalent interactions in the current model
(1) close submodels except for first one. Maybe something like command:
close #1.2-end
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/close.html>
(2) switch from ribbon to molecular surface of protein. Well, you probably want to do some coloring and other stuff besides just hiding ribbon and showing surface, which could be something like commands:
~ribbon surface protein
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html>
Or you could try a surface-showing preset, e.g.
preset ghost
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/preset.html>
(3) depends what you mean by showing interactions (lines? selection? coloring?). You should take a look at commands "contacts" and/or "hbonds" and choose the options that give what you want. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/hbonds.html>
You will need to spend some time trying the commands since there are an infinite number of possibilities for combinations of coloring and display styles and lighting and graphics effects. See also commands "lighting" and "graphics" and "set"
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/lighting.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/set.html>
... and the "making images" page with several relevant commands <https://rbvi.ucsf.edu/chimerax/docs/user/images.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 14, 2022, at 2:17 PM, Enrico Martinez via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Chimera's users! First I wish Happy New Year to everyone! I am just switching from Chimera to ChimeraX that I am going to use in no-gui (batch) mode to prepare screen shots of protein-ligand interactions based on the protein-ligand docking poses. Basically I am loading a pdb file of the complex (consisted of protein and ligand in multi-model format) from the terminal of my macOSX. I have a template for a batch file created in the bash script on the fly, that I used 2 years ago with an early version of ChimeraX.
# a batch file for chimeraX printf "open ${pdb} view; zoom 1.0; turn x 90; turn z -80; wait # options for appearance preset 'overall look' publication # set bg powder blue set silhouettes t; set silhouetteColor indigo; set silhouetteDepthJump 0.02
# make info of the screen 2dlab create title text \"${pdb_name}\" color red font gothic xpos .04 ypos .92 size 35
# options for light light depthcuestart .4 depthcueend .8; lighting full intensity 1.4 shadows true qualityOfShadows finer
save image ${structure}/${pdb_name}.png format png width 800 height 600 supersample 4 transparentBackground false wait exit" > chimeraX.${pdb_name}.cxc"
then I use it directly in terminal as chimerax-daily chimeraX.${pdb_name}.cxc"
may you suggest some commands that I may introduce into my batch file to 1) delete all models from the multi-model pdb file with the exemption of the first model. 2) switch from cartoon to surface representation of the protein 3) visualize protein-ligand non-covalent interactions in the current model
Yours with thanks Enrico
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