[Chimera-users] Contour plot of intersurf surface

[Elaine Meng]

Hello Miguel,
Seems like you could just take a screenshot of the MolSurfer display, if that is high enough resolution.

There are many good ideas, of course, but we only have limited resources to work on them!  However, I personally have never wished for a 2D projection of an interface. Instead I would just color the surfaces of the two parts forming the interface and then rotate them apart in opposite directions like an open book, to show complementarity.  There is an example of this "open book" approach in the image tutorials… although that tutorial does not color by hydrophobicity or electrostatics, you could imagine doing that, e.g. combining it with parts of the “surface properties” tutorial.

Opened Interface tutorial
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/openbook.html>
Surface properties coloring tutorial
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html>

Our group’s development effort is now in the ChimeraX program.  You may want to look at the “interfaces” tool in ChimeraX… see the “Interface Residue Plot” section at the bottom.  However, it does not currently show coloring by electrostatic potential or other properties.
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/interfaces.html>

Also ChimeraX is being structured for more outside development of plugins, with a Toolshed website that allows others to upload the plugins they wrote (i.e. if you would be interested in developing a plugin yourself) as well as download plugins from others.
<https://cxtoolshed.rbvi.ucsf.edu/>

If you become interested in ChimeraX, there is a separate chimerax-users at cgl.ucsf.edu mailing list you can join or just send questions.
<http://www.rbvi.ucsf.edu/chimerax/index.html>
<http://www.rbvi.ucsf.edu/chimerax/docs/contact.html>

Best,
Elaine

> On Feb 27, 2020, at 3:54 AM, Miguel Romero <miguel.romero at icvv.es> wrote:
> 
> 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,
> Miguel
> 
> 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