[phenixbb] ADP refinement selection

[Hena Dutta]

Hi,
I was trying to get one ADP per residue using the command as suggested in
the PHENIX document:

*Refining group isotropic B-factors*

One B-factor per residue:

% phenix.refine data.hkl model.pdb strategy=group_adp


See a part of my out pdb file (column 11):

ATOM   6971  C2  ADE F  15     -29.960 -20.547 -31.167  1.00 23.82      F    C
ATOM   6972  N1  ADE F  15     -30.382 -20.054 -32.336  1.00 24.20      F    N
ATOM   6973  C6  ADE F  15     -30.077 -20.702 -33.471  1.00 21.52      F    C
ATOM   6974  N6  ADE F  15     -30.496 -20.192 -34.629  1.00 20.08      F    N
ATOM   6975  C5  ADE F  15     -29.321 -21.893 -33.361  1.00 21.08      F    C
ATOM   6976  N7  ADE F  15     -28.823 -22.777 -34.307  1.00 22.85      F    N
ATOM   6977  C8  ADE F  15     -28.193 -23.670 -33.593  1.00 21.80      F    C
ATOM   6978  C2' ADE F  15     -27.648 -25.781 -31.357  1.00 22.11      F    C


But, I got different temperature factors for different atoms in the
same residue. Is that what I should get? How can I create one
temperature factor for each residue?

Regards...

Hena



On Thu, May 26, 2011 at 11:05 AM, Pavel Afonine <pafonine at lbl.gov> wrote:

> **
> Hi Christian,
>
> the problem is that you did not ask phenix.refine to refine the rest of the
> atoms isotropically (with your command below you only refine anisotropic
> ADPs of atoms in chain Q, and the B-factors of all the other atoms are not
> refined):
>
>      adp {
>       individual {
>         anisotropic = "chain Q"
>       }
>
>
> I would do it like this:
>
> adp {
>   individual {
>      anisotropic = chain Q and element CL
>      isotropic = not (chain Q and element CL)
>   }
> }
>
> Pavel.
>
>
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>
>
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