Just use a simple display by distance-zone command, in which you can put any distance you want, for example, waters within 5.5 Angstroms of protein: show solvent & protein :<5.5 see the help on how to specify distance zones <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#zones> The default initial display uses 3.6, as described in: <https://rbvi.ucsf.edu/chimerax/docs/user/autostyle.html> 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
On Oct 24, 2024, at 3:18 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Chimera X users !
I have a question about the visualization of water around the protein.
When I open the pdb + trajectory of the whale system, ChimeraX masks most of the water box, only showing some selected water molecules (probably involved in the interactions with the protein). Then, viewing the MD system, I can observe an exchange of this water, which is great ! Would it be possible via some command to modify the number of the displayed water in the beginning of simulation e.g. showing more water observed in the proximity to protein (..but still not the whole water box !) ?
Many thanks in advance
Enrico