[Chimera-users] Contour plot of intersurf surface

[Miguel Romero]

Dear Elaine,

Thank you very much for your detailed and usuful answers. You provide great support.

Cheers,
Miguel

El 27 de febrero de 2020 19:07:16 CET, Elaine Meng <meng at cgl.ucsf.edu> escribió:
>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
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