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 mailto:[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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