[Chimera-users] Showing Binding surface

Bobo Dang bbdang at uchicago.edu
Thu Jan 10 16:03:52 PST 2013


Hey Elaine,

You are right, I think I didn't make it clear before.

Here is where I got the different value:

 after surfcat, I selected the surface for d chain and use "measure volume
and area" in tools->surface and binding assays, then I got a area value,
that's where the difference come from.

the function "measure volume and area" just gives a volume and a area
value, it doesn't distinguish SAS or SES.

I checked the manual guide more carefully, it says this function gives the
"total surface area of a surface model", but again I don't really
understand how chimera define the model.

Thanks for your great help.

bobo



On Thu, Jan 10, 2013 at 4:25 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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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