[phenixbb] refinement of ligands and waters
pafonine at lbl.gov
Wed Jun 10 05:07:27 PDT 2015
> 1) I have a metal coordinated to a cofactor in the active center of my
> protein structure. The initial solution provided by
> phaser/autobuilding already contained the metal+cofactor modelled in
> the density but with zero occupancy. Then I created all the necessary
> restraints and cif files with phenix_ready_set and did two cycles of
> model building/phenix refinement. The refined structures always
> contained zero occupancy for those atoms. My question is: should I
> manually change the occupancy for the metal+cofactor to 1? I thought
> this would be made automatically by phenix because I selected the
> option “occupancies” and “individual B-factors” in the refinement
this is explained in the manual:
Please let me know if it is still not clear.
In a nutshell, if you want occupancy to be refined automatically it
needs to be between 0 and 1 in input PDB file.
> 2) When manually placing waters in the density with coot, what is the
> maximum value of B-factor that is acceptable for a water? I am asking
> that because I have some water molecules with weak density and
> consequently B-factors between 45 and 55 but that are involved in
> interactions with other molecules. Is it better to keep those waters
> or remove them?
No need to do it manually. Let phenix.refine update water
(add/remove/refine) and check them once or so at the end of refinement
to make sure all water make sense.
There are way more considerations that go into decision-making about
placing a water than just B-factor; typically they are considered all
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