The requirement sounds extremely suspect: every atom in the structure
contributes to every reflection, so refining "only some atoms" makes as
little mathematical sense as refining against "only a subset of
reflections".
Especially not Bfactors, which are after all where errors get pushed
into. So if you refine Bfactors for only some atoms, all you're doing
is making the refinement program shove all the errors in the *whole*
structure into the Bfactors of a few atoms. You'd have to explain
extremely carefully why those atoms deserve that -- and even then I
doubt anybody would believe you.
phx.
On 26/08/2010 22:19, Hailiang Zhang wrote:
Thanks a lot Ethan, I will give it a try.
Best Regards, Hailiang
On Thursday 26 August 2010 11:56:39 am Hailiang Zhang wrote:
Hi,
I want to refine B factors for several residues only (all the other B
factors and all coordinates fixed, I know it sounds weird but there is a
reason to try that).
Maybe you could tell us what this reason is?
Is there anyway CCP4 can do this? Thanks for any suggestions!
Suggestion 1)
Calculate structure factors for the entire rest of the model.
Include these as F_partial contributing to the refinement of a model
containing only your residues of interest. In this refinement,
refine only the B terms.
Caveat: I think you will encounter problems with how to handle
the bulk solvent correction. Perhaps that must be included in
F_partial also, and omitted from the subsequence mini-refinement.
Suggestion 2)
- Place your residues of interest in a single TLS group.
- Do not assign any other atoms or residues to a TLS group.
- Refine the entire model using refmac in TLS refinement mode.
Choose 5 or 10 cycles of TLS refinement, but 0 cycles of
coordinate/Biso refinement. Disregard all output other than the
refined TLS description for the B factors in your residues of
interest.
- Use TLSANL to expand the TLS parameters back to individual
Biso if you like.
Best Regards, Hailiang
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742
