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

Thank you Elaine! I played with it today and it looks great! Some additional questions (sorry for it at the first time the thing seems abit tricky): 1)may I automatically place the 2D label on the top left corner of the screen instead of manually defining its X-Y using xpos ypos? 2dlab create title text \"name_of_the_complex" color red font gothic xpos .04 ypos .99 size 40 2) assuming that I open 2 molecules in the same session open A.pdb open B.pdb then I remove all the models with the exemption of the first close #1.2-end How could I superimpose A to B (align the structures) and then hide cartoon from B.pdb (keeping only ligand) ? 3) Is there any possibility to put your signature on the screen-shot? like "Observed by Enrico Martinez" ? :-) Many thanks in advance!! Enrico сб, 15 янв. 2022 г. в 00:11, 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

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On Jan 14, 2022, at 3:03 PM, Enrico Martinez 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 :

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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...

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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

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On Jan 14, 2022, at 2:17 PM, Enrico Martinez via Chimera-users 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