[chimera-dev] About Backbone Dependent Library

[ylei at ecs.umass.edu]

Hi all

I am currently working on a project, which needs to rebuild the  
statistics using modified protein structures, say, some other set of  
proteins.

There is one quick question about interpreting the BBDep Library. What's
the exact definition of the fourth column "N" in the library file  
format? I thought for each residue within some (phi,psi) angle pair  
bin, it is the total number of sidechains found in all of the 850  
proteins. However, I checked ASN and GLN these two types of amino  
acids using "Chimera" to return the (phi,psi) dihedral angles for each  
ASN and GLN residue among 850 proteins with tens of exceptions which  
have no dihedral angles returned from Chimera(I just ignore them).  
Then, I count the number of sidechains for each (phi,psi) bin(10*10  
degree). It turned out that this number is not consistent with the "N"  
value in BBDep. e.g.  For ASN at bin (phi=-70,psi=-40), Chimera  
returns 372
sidechains in total from those 850 proteins, while BBDep says 2348.  
The difference is so large and very common over almost all the bins. I  
thought probably there might be some stupid errors in my understanding  
of the "N" value, but could you point that out for me? Or, did  
Dunbrack guys use another set of proteins other than those 850 ones?

Best regards and thanks,

Yang Lei

Electrical & Computer Engineering
University of Massachusetts, Amherst