[chimerax-users] [Chimera-users] ChimeraX in no-gui mode: visualisation of protein-ligand interactions

[Elaine Meng]

See the "color" command for coloring the ligand, and "set" or "graphics" for coloring the background, and "label" (or "2dlabels" but that usually requires you to position them interactively) for labeling.  All of these are included in the "making images" page I mentioned  near the end of my previous message.
Best,
Elaine



> On Jan 14, 2022, at 3:03 PM, Enrico Martinez <jmsstarlight at gmail.com> wrote:
> 
> Thank you very much, Elaine!
> I really like ChimeraX and it looks so great for me with all of those
> presents :-) I will look for the details regarding the options. Just a
> few addtional questions regarding customizing representation of
> protein-ligand interactions using ghost preset:
> In particular: I would like to color ligand (in orange??)
> To add labels (like Try-193) on the displayed side-chains around the ligands
> To change background from black to indigo!
> :-)
> Many thanks in advance!
> Cheers
> Enrico
> 
> пт, 14 янв. 2022 г. в 23:48, Elaine Meng <meng at cgl.ucsf.edu>:
>> 
>> 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 at 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
>> 
>