[chimerax-users] Chimera X -showing electrostatic potential

[Elaine Meng]

Dear Yi Shi,
The structure is nice work, and worth showing off!  We are fine so far... I hope you are well too.

To color a surface by electrostatic potential in ChimeraX, currently you need to use a separate program to generate the electrostatic potential map, for example the APBS web server or the DelPhi web server mentioned/linked to the Chimera tutorial here:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html#esp2>

After you generate the map (e.g. a .dx file, .phi file, or .cube file)
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#volume>

... then you can open it in ChimeraX and use it for coloring the protein molecular surface with the ChimeraX "color electrostatic" command: 
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#map>

If you open a .cube file it will automatically show as isosurfaces.  However, you can hide the isosurfaces such as by clicking the "eye" icon in the Volume Viewer panel, and then carry on with using the coloring command as mentioned above.  Of course, you need to open the protein structure and then display the protein's molecular surface first, e.g. with the "surface" command, Actions menu, or Molecule Display icon.
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html>

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 5, 2020, at 7:14 PM, Yi Shi <yi.shi at pitt.edu> wrote:
> 
> Dear Elaine,
> 
> Hope this finds you, your family and colleagues safe and well. 
> 
> We have a question about Chimera X software that you and your colleagues developed.  Do you know how to show the electrostatic potential using Chimera X? Do we need some external software to do this? 
> 
> BTW, the software that you developed was amazing that we really enjoy it. And thanks a million for using our Nup84 hybrid structure for the cover of your paper in Protein Science. Absolutely beautiful work!
> 
> Thanks in advance. 
> Yi
> 
> Yi Shi Ph.D.
> Assistant Professor
> Department of Cell Biology 
> Program for Integrative Systems Biology
> Pitt/ CMU Program in Computational Biology 
> University of Pittsburgh School of Medicine
> BST3 9049
> 3500 5th Avenue
> Pittsburgh PA 15213
> 412-383-3242 (office)
> 412-383-3243 (lab)
> www.shi-lab.org