[Chimera-users] Contour plot of intersurf surface

Miguel Romero miguel.romero at icvv.es
Thu Feb 27 03:54:16 PST 2020

Hello Elaine,

Thank you for your response. It's been very useful.

Yes, I am looking for something similar to MolSurfer's output: 2D 
projections of interface surfaces. The only problem I see with MolSurfer 
is that I have not been able to find a way to download the images of the 
2D projections yet.

Do you think those type of 2D projections could be done with Chimera? I 
am thinking, for instance, in generating the 2D projections from the 
vertex coordinates of the surface generated with Chimera intersurf 
command. Does it seem a good idea?

Thank you very much,

On 26/2/20 18:39, Elaine Meng wrote:
> Hi Miguel,
> I can’t think of a way to generate a 2D representation from the intersurf surface.  It is unclear to me exactly what you mean, however.  What are the contours showing?  If the 3D shape, why not just show as 3D?
> You may want to take a look at another program, MolSurfer, which generates 2D representations of hydrophobicity and electrostatic potential at an interface.  I never used it myself, but that is what the paper about this program (link below) shows.
> Molsurfer web server:
> <https://molsurfer.h-its.org/>
> Molsurfer paper:
> <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC168994/>
> 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 26, 2020, at 7:25 AM, Miguel Romero <miguel.romero at icvv.es> wrote:
>> Hello,
>> I am looking for a way to generate a contour plot from the interface surface generated with the intersurf command. The idea is to have a 2D representation of the interface. I would really appreciate any suggestion.
>> Thanks in advance,
>> Miguel

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