[Chimera-users] surface coloring by electrostatic potential; raytracing

Elaine Meng meng at cgl.ucsf.edu
Thu Jul 16 09:29:33 PDT 2015


Dear Leila,
I’m guessing you need to show the surface before you can color it, for example with command “surface” or menu: Actions… Surface… show.  Then the top part of the Coulombic Surface Coloring dialog should list the surface, and the Apply button should be active. Click the Help button on that dialog for more details about the tool.  

There is also a Chimera tutorial with surface coloring by electrostatic potential:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html>

In the image-saving dialog (File… Save Image) there is a Rendering option to either use Chimera or raytrace with POVray, but I strongly believe you can get better images withChimera without raytracing.  For example, if you like to see shadows, you can just turn them on interactively in Chimera using the Effects tool (Tools… Viewing Controls… Effects).  The POVray process from Chimera is fairly slow and in my opinion, usually gives images that are too dark with too much contrast.  

There is a list of tips for making good images here (also shown if you click the Tips button on the image-saving dialog):
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html#tips>

I changed the email subject line because “question” is not very informative.  I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Jul 16, 2015, at 3:16 AM, leila karami <karami.leila1 at gmail.com> wrote:
> 
> Dear chimera users,
> 
> 1) I want to have electrostatic surface of my protein in chimera. To this, I used Tools... Surface/Binding Analysis... Coulombic surface coloring
> 
> A new window is opened, but apply bottom is inactive.
> 
> 2) There are ray command in pymol to obtain better image of  molecular structures. Is there a similar command or utility in chimera?
> 
> Any help will highly appreciated.
> 
> Best wishes,
> Leila




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