Hi Hena,

1) refining group B-factor (one refinable B per group of atoms), phenix.refine does not change the mutual distribution of B-factors within the group. For example, if the original B-factors in the group were

10,20,30,40

after the group B-factor refinement they can be

10+b,20+b,30+b,40+b

where b is refinable parameter that can be any number that phenix.refine comes up with.

2) If you really want the B-factor to be all the same, then you need to reset them first to some meaningful number, say Wilson B or average B:

phenix.pdbtools model.pdb set_b_iso=50

then do refinement.

3) Note, that the default is

group_adp_refinement_mode = *one_adp_group_per_residue \
                                  two_adp_groups_per_residue group_selection

and if you change it to

group_adp_refinement_mode = one_adp_group_per_residue \
                                  *two_adp_groups_per_residue group_selection

phenix.refine will refine two B-factors per residue: one for side- and one for main-chain atoms of the residue.

4) For more details, see "On atomic displacement parameters..." article here:
http://www.phenix-online.org/newsletter/CCN_2010_07.pdf

5) In my experience highly restrained refinement of individual ADPs works almost always better than any of the group B refinement options mentioned above. phenix.refine uses unique type of restraints for individual isotropic B refinement that we introduced back in 2005: see above article for details.

Pavel.

On 7/15/11 12:17 PM, Hena Dutta wrote:
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 <[email protected]> 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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