Hi Radoslav, Yes, you can select or specify atoms by atom attribute "serial_number" ... but if the purpose is to select by solvent-accessible surface area, you could use the "measure sasa" command to assign atom attribute "area" and then specify by that instead. atom attributes <https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html> <https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html#atom> command-line specification by attribute value <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#attributes> measure sasa <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa> there is also a graphical interface to select atoms by attribute value ranges, menu: Select... By Attribute Value <https://rbvi.ucsf.edu/chimerax/docs/user/tools/render.html> or map a whole palette of colors to the values, menu: Tools... Structure Analysis... Render/Select by Attribute, or command "color byattribute" <https://rbvi.ucsf.edu/chimerax/docs/user/tools/render.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute> color palettes <https://rbvi.ucsf.edu/chimerax/docs/user/commands/palettes.html> Command examples: open 2gbp surf color @@serial_number=234 red measure sasa protein color @@area>25 yellow color byattribute area palette puor I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 31, 2024, at 9:11 AM, Radoslav Krivak via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi
I'm struggling with the following task. I want to display protein surface and color specific surface patches. More precisely, I want to:
For each surface patch: 1. select specific solvent exposed atoms (by "Atom serial number" column from pdb file) 2. assign their surface a custom color (different color for each patch)
A surface patch can contain atoms from 2 or more chains.
Basically I'm trying to achieve something that looks like this: https://raw.githubusercontent.com/rdk/p2rank/refs/heads/develop/misc/img/p2r...
Is that even possible in ChimeraX? If it's not possible to select specific atoms by atom serial number I'd like to do it at least for residues.
I’d be grateful for any help.
Best regards Radoslav Krivak
