[Chimera-users] Showing Binding surface

Elaine Meng meng at cgl.ucsf.edu
Thu Jan 10 14:25:55 PST 2013


Hi Bobo,
Maybe you were looking at the wrong numbers?  I bot 349 with both approaches, surfcat and measure buriedArea.

Here's what I did:

open 4gln
delete solvent
surfcat one :.d
surfcat two :.e
surf one
surf two
surfcat both :.d-e
surf both
start Reply Log

Reply Log shows total SASA (solvent-accessible surface area) values:
one 3772
two 6927
both 10,000

0.5 (3772 + 6927 - 10,000) = 349

measure buriedArea :.d :.e

... also gives 349

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 2:10 PM, Bobo Dang wrote:

> 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




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