[Chimera-users] Showing Binding surface
bbdang at uchicago.edu
Thu Jan 10 14:10:40 PST 2013
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
measure surface area of d, I got 2972.6,
I do the same thing for e,
surfcat 2 :.e
I got 5504;
then I do that for d,e as one model,
surfcat 3 :.d-e
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
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
> 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
> I hope this helps,
> 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:
> > <
> > (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
> > 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
> > <
> > 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>
> > <
> > Example Intersurf result is shown here:
> > <
> > 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
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the Chimera-users