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

Elaine Meng meng at cgl.ucsf.edu
Wed Apr 7 09:08:12 PDT 2010

Hi Yasser,
These are scientific issues that would probably be better answered by  
literature searching and reading some relevant papers, but here are my  

(1) Why use B-factor when SASA already directly describes the solvent- 
accessibility of atoms in the structure?  They are two different  
things.  Yes, you would often expect them to be correlated, but I  
don't see any reason to complicate your decision by considering B- 
factor.  There are factors such as crystal packing that would cause  
deviations from the expected correlation.  Personally, I would just  
use coloring by areaSAS or areaSES values (as mentioned in the earlier  
mail) in Chimera to decide on some cutoff, and then stick with it, or  
use the GetArea server to calculate % exposed and use that instead.

(2) I'm not aware of any commonly used B-factor cutoff, and it seems  
like the value would depend on what you were going to do after  
applying the cutoff.  I'm not even sure if the values from one  
structure can be compared to the values from another without some kind  
of normalization.

Other people may have different opinions, or more knowledge in this  
area, however!
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 7, 2010, at 8:24 AM, Yasser Almeida Hernández wrote:

> 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

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