Re: [ccp4bb]: How to deal with sidechainatoms with low electron density?

["Harry M. Greenblatt" <harry.greenblatt@weizmann.ac.il>]

***  For details on how to be removed from this list visit the  ***
***          CCP4 home page http://www.ccp4.ac.uk         ***

BS"D

Dear All,

In reply to Florian's question, it boils down to choosing between the  
lesser of two evils.  In the end, however, I agree with the method  
discussed by Bart:  delete parts of side chains not seen in electron  
density, and keep the residue name as it should be, even if you have to  
delete down to the CB.  These residues are flagged in the PDB file.   
Putting explicit side-chains where there is no clear density is  
misleading afterwards, since it gives the impression that something  
definitive is there, which is not the case.  Many non-crystallographers  
look at the pdb structures, and don't appreciate what high B-factors  
mean, especially when the mean B-factor for the side chains is not  
considered.  In other words, B-factors in the 60's for a side-chain in  
a structure where the mean B-factor is 20, probably indicates little or  
poor density, but if the mean B is 45, the density might be quite  
reasonable.  So one cannot rely on B-factors alone to act as flags for  
side chains with no/poor density.

Harry

------------------------------------------------------------------------ 
-------------------------
Harry M. Greenblatt
Research Associate
Dept of Structural Biology			harry.greenblatt@weizmann.ac.il
Weizmann Institute of Science		Phone:        972-8-934-3625
Rehovot, 76100 				Facsimile:   972-8-934-4159
Israel