[Chimera-users] Interaction interface between two residues and measure buriedArea

Elaine Meng meng at cgl.ucsf.edu
Wed Mar 11 09:37:27 PDT 2015


Hi Massimo,
(1) I am not aware of any clear-cut rules of which to use for what purposes.  SES is where the probe sphere (crudely representing water) touches, SAS is where the probe sphere center can go.  There have been some efforts to derive an energy value per unit area of hydrophobic surface buried, so if you were using that kind of multiplier you would of course use the measure for which it was developed.  Otherwise, you could just think about the geometric definitions and see if one or the other fits what you are trying to measure.  There are some pictures on the web illustrating the difference, e.g. Fig 3 here:
<http://ieeexplore.ieee.org/ieee_pilot/articles/06/ttg2009061391/figures.html>

(2) The fallback warning is something about certain calculations failing so that only a single component (e.g. outer envelope and not interior bubbles) is calculated, but it would still show up as a warning in the Reply Log, so I wouldn’t worry about the specifics.  I believe it is rare, but sometimes there are errors or visible singularities in the surface that occur without a warning going to the Reply Log.  I don’t think we can do or say much about this.  In Chimera, molecular surfaces are created with embedded software from the MSMS package.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces>

One issue is that you are stretching the functionality beyond its intended purposes.  Measure buriedarea was mainly intended for looking at intermolecular or interdomain interfaces, not for measuring the area of single residues packing against each other within a protein.  When you are using it on these smaller subparts, possibly with more tortuous shapes, I imagine there would be a greater chance of errors.

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 Mar 11, 2015, at 5:24 AM, ms <devicerandom at gmail.com> wrote:

> Dear all,
> I am trying to understand what is the area buried between two residues (or between one residue and two other ones) in several structures. It seemed to me the best way to do this was to use the command "measure buriedArea :res1 :res2" on the full structure (once all non-protein components have been cleaned out of it). The overall trend of these measures seems consistent with visual inspection.
> 
> However I have a couple of questions about it:
> 
> 1) I am unsure about what value is best to use/compare, buriedSAS and buriedSES. It seems to me that the difference between the two is essentially in the geometrical protocol used. Is there any general wisdom about what do they physically mean and how should I approach each value?
> 
> 2) In some cases I receive *negative* values for buriedSAS and/or buriedSES. Looking on the ML it seems that it is a symptom of a buggy or failed area calculation (e.g. http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-April/005119.html ). However it also says that I should see a "fallback" warning on the Reply Log -I see nothing of the sort. How do I troubleshoot this? Also in cases where the calculated value is positive, how can I be sure that the values are indeed meaningful?
> 
> Any other feedback on the kind of measurement I am trying to do is more than welcome.
> Thanks a lot,
> Massimo




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