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

[Phoebe Rice <price@midway.uchicago.edu>]

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

Several years ago I stopped truncating side chains when I realized that my 
favorite electrostatics-calculating program assigned charges based on atom 
type, not residue name, so that floppy K's, etc were becoming neutral.  I 
suppose you can't perfectly model a charge when you don't really know where 
it is, but a slightly misplaced charge seems better than no charge.  Is 
this still a worry?
         Phoebe

At 05:52 PM 11/24/2002 -0600, you wrote:
>***  For details on how to be removed from this list visit the  ***
>***          CCP4 home page http://www.ccp4.ac.uk         ***
>
>On Sun, 24 Nov 2002, Harry M. Greenblatt wrote:
>
> >...
> > 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.
> >...
>
>Is this not exactly what one does when the main chain cannot be seen in
>the electron density map?  That is, we seem to have no problem depositing
>structures with missing residues/atoms at the N- and C-termini and in
>loops.  Why not be consistent and do the same for other atoms that cannot
>be visuallized or modelled?

Phoebe A. Rice
Asst. Prof., Dept. of Biochemistry & Molecular Biology
The University of Chicago
phone 773 834 1723
fax 773 702 0439
http://molbiol.bsd.uchicago.edu/faculty/pRice/index.html
http://bmb.bsd.uchicago.edu/