Hi Pete,
when you ask phenix.refine to do group ADP (B-factor) refinement, there
are three possible options:
- phenix.refine refines one isotropic B per residue (done by default);
- phenix.refine refines two isotropic B per residue;
- phenix.refine refines one isotropic B per user-defined group of atoms
(where number of groups can be any).
Obviously, in there is no need to list (in PDB header or in .log file)
groups for the first and second options, since it is obvious.
In the third option a user provides atom selections for the groups, so
they are listed in a parameter file and therefore listing them in .log
or in PDB files will be redundant (although may not be a bad idea to
keep track).
Why don't you ask the authors of that published structure?
Pavel.
On 10/22/09 3:04 PM, Pete Meyer wrote:
> Does anyone know offhand if or where the ADP groups used in refinement
> are listed in the PDB headers? I've found TLS groups and NCS groups,
> but nothing about which residues are in the ADP groups.
>
> I'm trying to figure out exactly what was done in a published
> structure, and don't currently have a functional copy of phenix to
> test with.
>
> Pete
|