[Chimera-users] Surface mesh and coloring queries

[Elaine Meng]

Hi Bala,
(A) see menu: File… Export Scene (or command “export”).  There are several formats that can include surfaces.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/export.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/export.html>

(B) The surface coloring by map value (density, electrostatic potential, etc.) uses the map grid-point positions and values compared to the positions of surface vertices.  You can also get the values interpolated to atom positions with the Values at Atom Positions tool.  These all use trilinear interpolation, which is a very common general algorithm.  See “Data value interpolation” near the bottom of this page:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html>

For more details, you could just google “trilinear interpolation”… for example, there is a page at wikipedia:
<https://en.wikipedia.org/wiki/Trilinear_interpolation>

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

> On May 29, 2018, at 3:16 AM, Bala subramanian <bala.biophysics at gmail.com> wrote:
> 
> Dear Chimera friends,
> 
> Good day. Please enlighten on the following queries,
> 
> a) I would like to know if I can write the surface mesh calculated within chimera to a file. From the documentation of the surface command, it seems that it is not possible. My idea is to have the vertices and faces as outputs to be fed to a plotting tool aimed for webpage display. Please guide me if this is possible or the related source code I can modify to have the output.
> 
> b) How does chimera color surfaces, for instance, coulombic surface. What I am not understanding is the way the surface colors are interpolated to atomic charges. I would like to adopt the method for my plotting purpose.
> 
> Thanks in advance,
> Bala