Hi Eric, If you spend a little time learning the program you will be able to generalize a bit more. There are several tutorials. <https://www.rbvi.ucsf.edu/chimerax/tutorials.html>
On Dec 5, 2024, at 2:57 PM, Eric Martz via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Consider this:
open 1pgb fromDatabase pdb format mmcif style sphere show atoms
1. What is the command to hide all water?
hide solvent - or - hide :HOH Almost all commands use "atomspec" which has a lot of options, element (as in your previous question), residue name, category such as "solvent" etc. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html> If you don't want to learn commands you can use the menu, Select... Residues... HOH Actions... Atoms/Bonds... hide
2. How do I color charged amino acids, leaving uncharged one a neutral color (such as white)?
I was hoping there was a menu item or command that would do something similar to this:
color all white color :lys,arg blue color :glu,asp red color :his lightblue
without having to type all those commands.
You can make your own presets which are sets of commands that are read from a file. Then you can just choose your custom entry from the Presets menu. See the "Startup" section of the preferences. <https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup>
FirstGlance in Jmol and iCn3D have "one click" ways to do this, but I don't see one in ChimeraX or MolStar.
Thanks, -Eric
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco