The problem is the unrestrained nature of the grouped b-factor
refinement itself. Read this thread
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In a nutshell, just stick with (properly wighted) individual B-factors.
On Fri, 2010-07-16 at 10:57 -0400, hongjunyu wrote:
> Hi,
> I am using CNS to refine the structure.But when I come to bgroup refinement, the
> produced bgroup.pdb have many residues with very high B factor. I read the
> bgroup.inp, and found the item‘B-factor groups'with following description:
> {* select atoms in group 1 - protein mainchain example *}
> {===>} bg_group_1=((resname ALA or resname ARG or resname ASN or
> resname ASP or resname CYS or resname GLN or
> resname GLU or resname GLY or resname HIS or
> resname ILE or resname LEU or resname LYS or
> resname MET or resname MSE or resname PHE or
> resname PRO or resname SER or resname THR or
> resname TRP or resname TYR or resname VAL or
> resname HISH or resname HISU or resname M3L or
> resname CPR) and
> (name c or name n or name ca or name o or name ot+));
> The atom name description seems different from the corresponding name in the pdb
> (capital and small letter). Is it the problem? Should I update the atom name
> description?
>
>
> Hongjun Yu
--
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
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