[chimerax-users] render buriedArea surface?

[Alexis Rohou]

Thanks Elaine,

I wonder if I am missing something, but I'm not sure how the
atom-selection-based methods can be used to accurately depict the buried
surface area. The problem is that an atom is either in the selection or out
of it, and then all of that atom's surface gets colored, not the just the
regions of the surface that were buried.

See for example this screenshot:
[image: image.png]

Here, I wanted to color the buried surface between the yellow chain and the
purple one. I followed the method you outlined , which correctly identified
that most of the atoms for the Tyr side chain I am showing are involved in
a contact with the purple chain. But clearly, not all the blue surface is
buried by the purple chain - only the "top" and "left parts of it, in this
view.

For the record, here's what I did:
color #1 fromatoms target s transparency 50
measure buriedarea name_yellow with name_purple sel true cutoff 60
color sel & name_yellow  blue target s transparency 50

Am I misunderstanding something? Or in fact, should I just use method #3
from the Chimera tutorial instead?

Thanks for your guidance!

Cheers,
Alexis



On Mon, Sep 9, 2019 at 10:27 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> There’s a nice diagram explaining SAS vs. SES in the “surface” manpage:
>
> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#top>
>
> > On Sep 9, 2019, at 10:24 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> >
> > Hi Alexis,
> > The “measure buriedarea” command has a “cutoff” option that can be used
> with its “select” and/or “color” options to select and/or color atoms with
> more than the specified cutoff area buried.
> > <
> http://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea>
> >
> > If you use the selection approach, you can then color the corresponding
> patches within the molecular surface, or hide the rest of the surface,
> etc.  For example, 1avx trypsin complexed with trypsin inhibitor:
> >
> > open 1avx
> > split
> > measure buriedarea /a&protein with /b&protein sel true cutoff 5
> > surf
> > color sel & /a red target s
> > color sel & /b yellow target s
> >
> > Note that “measure buriedarea” values are SASA (solvent-accessible
> surface area) whereas the displayed surface is instead the SES
> (solvent-excluded surface).  Larger cutoff values will select smaller
> patches that look more like the touching parts of the SES.  The “&protein”
> stuff is needed so that waters are not included in the calculation.
> Alternatively, you could “delete solvent” first.
> >
> > There are other ways to select the contacting atoms, e.g. with the
> “contacts” command, but this is the way based on surface area.
> >
> > There is a Chimera (not ChimeraX) tutorial that does exactly this same
> thing, with three different ways of identifying the interface atoms, and
> several other steps for making a figure to show the interface-surface
> coloring, like opening the interface like a book:
> > <
> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/openbook.html>
> >
> > The ChimeraX approach I outlined above is slightly different than method
> 2 in that tutorial, but also based on surface area.  Method 1 in that
> tutorial is analogous to using ChimeraX “contacts” command, but there is no
> ChimeraX equivalent for method 3.
> >
> > The other steps like opening the interface like a book can also be done
> in ChimeraX but the commands and/or their syntax would be different:
> ChimeraX does not have “set independent” for independent rotation, but
> relevant commands would be: move, turn, view name, view.  In the example
> above, I used “split”  so that the two chains are two models that can be
> moved separately with the move and turn commands.  You don’t need split to
> do the coloring above, but I saw that doing split afterward nuked the
> existing surfaces, which would defeat the purpose.
> >
> > 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 9, 2019, at 9:27 AM, Alexis Rohou <a.rohou at gmail.com> wrote:
> >>
> >> Hi all,
> >> I would like to depict the buried surface area between two chains. I
> have used "measure buriedarea" to measure it, and I can use "surface" to
> display the surfaces of either set of atoms, but I'd like to depict the
> surface of one of the chains, highlighting the region buried by the other
> chain.
> >>
> >> Is there a way to do this in ChimeraX?
> >>
> >> If not, does anyone have a recommendation as to how to achieve this?
> Perhaps by pre-computing the surfaces in another program?
> >> Thanks in advance!
> >> Cheers,
> >> Alexis
> >
> >
> > _______________________________________________
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> > ChimeraX-users at cgl.ucsf.edu
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> >
>
>
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