[Chimera-users] [Re: Residue exposition cutoff]

[Yasser Almeida Hernández]

Thanks for your answer...
About this i have an idea resumed in two question:
In principle an solvent-exposed residue must have in average high  
value of b-factor, so will be very flexible.

1 - Can i say that those residues that have and average b-factor up to  
a cutoff value AND an areaSAS (or % of that area) superior than a  
other cutoff value, will be exposed to the solvent???

2 - There is a cutoff value of b-factor for the residues flexibility?

Best regards


-------- Forwarded Message --------
From: Elaine Meng <meng at cgl.ucsf.edu>
Reply-to: Chimera BB <chimera-users at cgl.ucsf.edu>
To: Yasser Almeida Hernandez <almeida at cim.sld.cu>
Cc: Chimera BB <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Residue exposition cutoff
Date: Mon, 5 Apr 2010 11:22:37 -0500

Hi Yasser,
Actually you don't have to use DMS ... if you show a surface in
Chimera it also automatically computes the SES (solvent-excluded
surface) and SAS area per atom and per residue, attributes named
areaSES and areaSAS.  For more details, see these previous posts:
<http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-November/003291.html
  >
<http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-February/003597.html
  >

Some notes about areaSES and areaSAS:
(1) if you don't want to include inside bubbles in the surface area
calculations, after creating the surface(s) remove the inside bubbles
with the command:  setattr s allComponents false
(2) the surface that Chimera displays is the SES (also known as
Connolly surface or molecular surface), not the SAS, although both
sets of areas are calculated

Actually Tom Goddard mentioned the areaSAS attribute briefly in an
earlier reply to you:
<http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-June/003995.html>

As to what cutoff should be used for classifying atoms or residues as
buried or exposed, I'm not aware of any commonly used value.  It is a
more philosophical issue that depends on your ultimate purpose.  You
might try coloring by different cutoffs to try to decide what is
appropriate for your research (keeping in mind that the SES is what
Chimera actually displays), or read publications of similar work to
see what other researchers have used.  In publications, I have seen
residues classified by "fraction" or % of the surface area of a
residue in the structure divided by the area of that same type of
residue in a hypothetical fully exposed state, but I don't remember
the exact cutoffs used, and Chimera does not provide the fully exposed
values.  An example of a program that does provide such values is
GetArea:
<http://curie.utmb.edu/getarea.html>

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 Apr 3, 2010, at 1:38 PM, Yasser Almeida Hernández wrote:

> Hi all....
> I have 2 question, beyond Chimera's issues.
>
> 1 - There is some cutoff value to consider a residue or more   
> strictly, an atom exposed to the solvent?.
>
> 2 - Could i set a this cutoff using the area values and types (SR0,   
> SC0 and SS0) from the DMS program output?
>
> 3 - Wich program you recommend to compute SAS?
>
> Thanks,
> best regards




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-- 
Yasser Almeida Hernández, BSc
Center of Molecular Inmunology (CIM)
Nanobiology Group
P.O.Box 16040, Havana, Cuba
Phone: (537) 214-3178
almeida at cim.sld.cu

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