[chimerax-users] Re: Surface representation for small compounds

MAny thanks Elaine ! Actually the molmap is a great option, and it does what I need. I noticed that it always displays a "frozen" map selected for a particular frame in the case of multi-frame pdb. Would it be possible to update the generated map for each frame of my multi model pdb visualized as the md trajectory (open ./trajectory.pdb coordset true) ? Yours with thanks Enrico Il giorno gio 8 feb 2024 alle ore 23:28 Elaine Meng ha scritto:

Hello, This works fine for me:

open 1gcn surf surf style dot

However, the dot style can be very hard to see since the linewidth (dot size) is small and you cannot increase it, and/or the surface vertices are spaced rather far apart.

Here are two ideas for making a low-resolution surface for atoms:

(A) instead of a standard molecular surface, make a gaussian surface by using "surface" with the "resolution" option https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html

- OR -

(B) try making a density map from the ligand with "molmap" ... then you can adjust the isosurface level, etc. like for other density maps https://rbvi.ucsf.edu/chimerax/docs/user/commands/molmap.html

See the help links above for additional options such as to control vertex spacing of these surfaces.

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

...

On Feb 7, 2024, at 2:06 AM, Enrico Martinez via ChimeraX-users wrote:

Dear ChimeraX users

I am also experimenting on the representation of the surfaces of small compounds

surface ligand gridSpacing 0.5 probeRadius 1.2 color ligand white target s transparency 90

This creates a relatively large transparent surface around the small compound. How would it be possible to reduce the volume of the surface ?

Also I did not understand how to change the style of the surface among dot/mesh etc since adding style dot did not work.

I would appreciate any further creative examples of how to change the representation of a small compound in the case when I need to make it more "coarse-graining" , hiding some precise details of the structure ?

Many thanks in advance !

Enrico