[Chimera-users] Showing Binding surface

[Bobo Dang]

Thanks for the explanation, but still one more thing confuse me.

Indeed weather delete waters first then measure buriedArea, or just
use measure buriedArea :.d&protein :.e&protein command gave BaveSAS 349.

But when I use surfcat, I mean I delete waters first.

then use command

surfcat 1 :.d
surf 1

measure surface area of d, I got 2972.6,

I do the same thing for e,

surfcat 2 :.e
surf 2

I got 5504;


then I do that for d,e as one model,

surfcat 3 :.d-e
surf 3

I got 8117.6.

>From these values I do the calculation (2972.6+5504-8117.6)/2=179.5.

This value does not match with BaveSAS 349.4, or BaveSES 186.2.

Do you know where the difference come from? Does chimera define different
surfaces based on different methods?

thanks a lot

bobo

On Thu, Jan 10, 2013 at 1:54 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Bobo,
> One issue to be careful about with both "surfcat" and "measure buriedArea"
> is to NOT include stuff like waters.  I forgot to mention that issue in my
> first reply.  You could either delete water first, or when using the
> commands take care to use specifications that exclude water, something like
> this:
>
> measure buriedArea :.d&protein :.e&protein
>
> (because there are waters with chain ID D and waters with chain ID E)
>
> When I did that, I got the same answer both ways, BaveSAS 349 for 4gln
> protein-only.
> I hope this helps,
> Elaine
>
> On Jan 10, 2013, at 11:14 AM, Bobo Dang wrote:
>
> > Thanks a lot.
> >
> > Your method B is exactly what I want to get.
> >
> > As for the binding area, it seems that using different methods, I get
> different values.
> >
> > I tried surfcat command to get the surface area of D, E and DE. and then
> calculate by (D+E-DE)/2, it gave me 363. but using "measure buriedArea"
> command it gave me 372 for BaveSAS. Do you know why these two results are
> not the same even though the difference is small?
> >
> >
> > thanks
> >
> > bobo
> >
> > On Thu, Jan 10, 2013 at 11:59 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > Hi Bobo,
> > (A) If you mostly want the area measurement (not display), you can just
> use the command "measure buriedArea."  Use the Favorites menu to show the
> Chimera command line.  Structure 4GLN has 4 chains: D, E, F, and H ... I
> could see that by rainbow-coloring each chain a different color, for
> example with Chimera commands:
> >
> > open 4gln
> > rainbow chain
> >
> > You can see which chain is which by putting the mouse cursor over them,
> which will show an information "balloon."  So for example, I could measure
> area between chains E and F with:
> >
> > measure buriedArea :.e  :.f
> >
> > ...or between D+E and F+H with:
> >
> > measure buriedArea :.d:.e  :.f:.h
> >
> > The information goes to the Reply Log (show using Favorites menu).  For
> details on this command, see:
> > <
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#buriedArea
> >
> >
> > (B) If you care about display too, then more steps are required. By
> default, Chimera will make one surface that includes all the protein
> chains.  The "split" command will put each chain in a separate model, for
> example:
> >
> > split
> > surface
> > rainbow model
> >
> > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/split.html>
> >
> > You can see what models you have by showing the Model Panel (also in
> Favorites menu).
> >
> > Then you still want to show just the interface.  For example, to show
> only surface of E within 1.5 Angstroms of surface of F:
> >
> > ~surface
> > measure contactArea #0.2 #0.3 1.5 color orange offset 0.1
> >
> > <
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#contactArea
> >
> >
> > I had to look in the Model Panel to see what model numbers to use for
> the "measure contactArea" command.  If offset is >0, this command will make
> a new model, also listed in the Model Panel. To also show the whole surface
> of E, for example, you could use the command:
> >
> > surface :.e
> >
> > (C) instead of B, a completely different approach is to use the
> Intersurf tool to show an interface surface instead of the molecular
> surface of either chain.  This tool is in the menu under Tools...
> Surface/Binding Analysis.  In that dialog you would choose the two chains
> and then Apply.   You can use the histogram at the bottom to color by
> distance. You could also use the command "intersurf" to do the same thing.
> > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/intersurf.html>
> > <
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/intersurf/intersurf.html
> >
> >
> > Example Intersurf result is shown here:
> > <
> http://www.cgl.ucsf.edu/chimera/ImageGallery/entries/alphabeta/alphabeta.html
> >
> >
> > The Intersurf results are more "chunky," not as smooth as the molecular
> surface(s) shown by method B above.
> >
> > I hope this helps,
> > Elaine
> > ----------
> > Elaine C. Meng, Ph.D.
> > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> >
> > On Jan 10, 2013, at 8:21 AM, Bobo Dang wrote:
> >
> > > Dear Chimera Users,
> > >
> > > I am trying to use Chimera to show the binding surface between two
> chains in one Model and measure the area of this binding surface,
> > >
> > > but I don't know how I can select the bind surface, could anybody give
> me a hand? the model I am using is 4GLN from PDB.
> > >
> > > thanks a lot
> > >
> > > bobo
> >
> >
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
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