Dear Yiwen,The "surface" command shows a molecular surface (smoothed to probe radius), not the VDW surface.
However, with the "enclose" option you can get an enclosed molecular surface shown as mesh, if that is good enough, and you can also try using a smaller probe radius and finer grid, for example for residue 91 in chain A:
open 2gbp
surf :91 enclose :91 probe 0.25 grid 0.3
surf style mesh
Another point is that maybe you only want the surface on the sidechain, not the whole residue:
surf :91 & sideonly enclose :91 & sideonly probe 0.25 grid 0.3
surf style mesh
("sideonly" omits CA... if you want CA included, use "sidechain" instead)
The "sphere" representation shows the VDW surface. However, there is no simple way to show atoms as both sticks and spheres at the same time. For that approach, you would need to open the structure twice and show one copy as sticks and the other one as spheres, and make the spheres transparent.
Example:
open 2gbp
open 2gbp
style #2 sphere
transparency #2 60 target a
However, that is not very similar to your picture.
One reason is that transparency is not rendered completely correctly, you will only get a simplified view in which only the topmost transparent object is shown. So you can see nontransparent sticks behind the transparent spheres, but you cannot see other transparent spheres behind the frontmost transparent spheres.
Another reason is that ChimeraX does not have the option to show spheres with mesh. Only molecular surface can be shown as mesh.
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 Apr 25, 2024, at 11:15 PM, 我就要柠乐 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Sir/Madam
Recently, I have been using ChimeraX for graphical analysis, and I find the software to be very user-friendly and efficient. I am currently facing a challenge where I want to display the van der Waals surface of a residue, similar to this illustration（https://doi.org/10.1038/s41467-022-31526-7）.
<60374065@1BDB1249.6F462B66.jpg>
However, I am not quite sure how to write the command correctly. I have looked up the commands on the official website and tried using these two:surface #1:230； surface style mesh.
<F9D6355E@B9FDB55D.6F462B66.png>
The bottom is open （the rad circle）, but I would like to have a complete van der Waals surface with closed openings, similar to what is typically seen in the literature. I would appreciate your assistance. Thank you！
yours sincerely
yiwen
我就要柠乐
790639436@qq.com