[phenixbb] ADP refinement selection
Pavel Afonine
pafonine at lbl.gov
Fri Jul 15 12:34:28 PDT 2011
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 <pafonine at lbl.gov
> <mailto: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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