[Chimera-users] Showing Binding surface

Elaine Meng meng at cgl.ucsf.edu
Thu Jan 10 09:59:41 PST 2013


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




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