Ah okay, thank you ! Enrico Il giorno ven 25 ott 2024 alle ore 17:12 Elaine Meng <meng@cgl.ucsf.edu> ha scritto:
If you read the "initial display" page it says it is 3.6 angstroms only near ligand and metal ions, not the whole protein.
<https://rbvi.ucsf.edu/chimerax/docs/user/autostyle.html>
Of course you can use whatever distance you want, based on whichever atoms you want (ligand, or protein, or specific residues, etc.)
Elaine
On Oct 25, 2024, at 6:30 AM, Enrico Martinez via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Thank you very much Elaine !
Just one more question about the distance cut-off:
show solvent & protein :<3.6 ( the default distance value indicated in the manual) produced a very dense water layer around the protein containing much more water molecules compared to the default scene (shows only few water possible involved directly in the interactions). I could achieve better results with a much smaller cut-off show solvent & protein :<0.8 which still contains many water molecules but looks more realistic for visualization of md trajectory...
Yours with thanks
Enrico
Il giorno gio 24 ott 2024 alle ore 17:48 Elaine Meng <meng@cgl.ucsf.edu> ha scritto: 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
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