[phenixbb] Rotamers of unnatural halogenated amino acids

Pavel Afonine pafonine at lbl.gov
Mon Sep 26 16:58:56 PDT 2016

Hi Anna,

> I’m working on the refinement of a protein mutated with an unnatural 
> amino acid that contains one bromine atom. This particular amino acid 
> is present as two rotamers. I’ve managed to introduce and do 
> refinements with these two unnatural, brominated rotamers in Phenix, 
> but the problem is that when shooting the protein with X-rays about 
> 30-40% of the bromine atoms get knocked off. This means that the sum 
> of the occupancies for the bromine atoms of the rotamers needs to be 
> less than 1.00. However, the total occupancy of all the other rotamer 
> atom pairs must be 1.00. Is there a way in Phenix to refine rotamers 
> of brominated, unnatural amino acids, and at the same time have the 
> total occupancy less than 1.00 for the Br atoms only? Any advice how 
> to solve this is welcome.

the answer is in this newsletter article:

13 typical occupancy refinement scenarios and available options in 

Basically, all you need to do is to define each residue side chain 
conformer as one constrained group consisting just that one conformer. 
This will override the default behavior which groups occupancies and 
make them to add up to 1. One way of doing this is to compose a 
parameter file that looks like this, occ_params.eff:

refinement {
   refine {
     occupancies {
       constrained_group {
         selection = chain A and resseq 123 and altloc A
       constrained_group {
         selection = chain A and resseq 123 and altloc B

and load it into the GUI along with all other files (PDB, reflections, 
etc). This will refine one occupancy for "chain A and resseq 123 and 
altloc A" and one occupancy for "chain A and resseq 123 and altloc B", 
and they will not be related to each other. Each of the two occupancies 
will be free to refine to any value between 0 and 1.

Alternatively (instead of using parameter file), you can use Atom 
Selection Editor: Refinement Settings -> Select Atoms -> Refinement 
Strategy -> Group Occupancies -> Add Group.

Let me know if you have any questions or problems!


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