[Chimera-users] Calculating surface area

[Yangqi Gu]

Thank you very much!
Best,
Yangqi

On Friday, September 14, 2018, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Yangqi,
> Oh you said visualize, so I didn’t answer about measuring the area.  To
> measure the area based on molecular surfaces calculated from the atoms, see
> command
>
> measure buriedArea
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/
> measure.html#buriedArea>
>
> If you want a specific answer, make sure to ask a specific question!  :-)
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Sep 14, 2018, at 1:41 PM, Yangqi Gu <yangqi.gu at yale.edu> wrote:
> >
> > Hi Elaine,
> > Thank you for your reply. I guess my question is essentially to
> calculate the surface area. I am just wondering if we could extract that
> information from EM potential map. Such as inserting a plane where the
> interface locates and calculate the projection to the plane from the 3D
> volume. But I guess based on atom coordinates will be much more accurate.
> > Best,
> > Yangqi
> >
> > On Friday, September 14, 2018, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > Dear Yangqi
> > I may not understand your question completely, but from the atomic
> coordinates, you can just show the surfaces of each monomer and color the
> interface where the two surfaces are close to each other.  For example, see
> this image tutorial:
> > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/
> tutorials/openbook.html>
> >
> > As in that tutorial, if both monomers are in one file, to get separate
> surfaces instead of one combined surface, you may need to use “split” or
> put them in separate files first (the other way is to use the “surfcat”
> command if you’d rather keep them as one model0.
> >
> > However, there are lots of ways to find and/or visualize an interface,
> such as by H-bonds or contacts.  See FindHBond (or findhbond command), Find
> Clashes/Contacts (or findclash command, which is used in the tutorial
> above), and the Structure Analysis tutorial with examples of using those
> tools.
> > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/
> findhbond.html>
> > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/
> findclash.html>
> > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/
> tutorials/squalene.html>
> >
> > Additional related features that may interest you:
> >
> > - command “measure contactArea” which also shows a colored surface patch
> similar to that in the first tutorial above
> > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/
> measure.html#contactArea>
> >
> > - Intersurf tool:  shows a single “interaction surface”
> > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/intersurf/
> intersurf.html>
> >
> > I don’t know how you would use an EM map to visualize an interface
> surface.
> > I hope this helps,
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D.
> > UCSF Chimera(X) team
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> >
> > > On Sep 14, 2018, at 12:02 PM, Yangqi Gu <yangqi.gu at yale.edu> wrote:
> > >
> > > Dear Chimera users,
> > > I am trying to visualize the interface surface of my two monomers. Is
> there anyway to show the interacting surface from Chimera by using the EM
> map? Or should I do it from PDB coordinates?
> > > Best,
> > > Yangqi
> >
>
>

-- 

Yangqi Gu
Graduate Student
Malvankar Lab
Yale University, West Campus
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