[chimerax-users] Chimera X -showing electrostatic potential

[Yi Shi]

Thanks again!
Yi



On Wed, May 6, 2020 at 1:52 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> I forgot to mention that coloring the surface by electrostatic potential
> is also covered in a ChimeraX tutorial here:
>
> <
> http://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html#esp
> >
>
> If you open this tutorial in the ChimeraX browser, such as with command:
>
> open
> http://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html#esp
>
> ... then clicking the links will execute the commands in ChimeraX!
>
> Elaine
>
> > On May 5, 2020, at 7:50 PM, Yi Shi <wally.yis at gmail.com> wrote:
> >
> > Awesome, thanks!!!
> > Yi
> >
> >
> >
> > On Tue, May 5, 2020 at 10:45 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > 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
> >
> > _______________________________________________
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> > ChimeraX-users at cgl.ucsf.edu
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>
>
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