[phenixbb] Water/residue alternative conformations

Pavel Afonine PAfonine at lbl.gov
Mon Jun 8 11:48:06 PDT 2009

Hi Roeland,

if you have a triple conformation A, B and C, then their occupancies 
should be qA+qB+qC=1. Now if you get a water that is coupled with altloc 
C, then qHOH+qC=1.
Currently you cannot do it in phenix.refine, sorry. In fact, you can 
make it running, but currently I think it will do something  different 
from what one would expect. Say you have this artificial molecule in PDB 
file, that mimics your case:

ATOM      1  O  AHOH H   1       8.767   5.853   7.671  0.30 
10.00           O
ATOM      2  O  BHOH H   1       7.767   7.853   7.671  0.50 
12.00           O
ATOM      3  O  CHOH H   1       7.767   5.853   5.671  0.20 
19.00           O
ATOM      4  K       H   2       7.000   5.000   7.671  0.80 
25.00           K

then what you want to do is defined by the following selections:

refinement {
  refine {
    occupancies {
      constrained_group {
        selection = resseq 1 and altloc A
        selection = resseq 1 and altloc B
        selection = resseq 1 and altloc C
      constrained_group {
        selection = resseq 1 and altloc C
        selection = resseq 2

Unfortunately, for the moment the automatic procedure outsmarts itself 
and automatically removes "altloc C" selection from the first group 
since it is present in the second group, and therefore the algorithm 
"thinks" it is a duplicate unwanted selection. I will fix it once I get 
a chance (it is not an easy-fix).

However, with some manual work you can approximate what you want to do. 
Refine that triple conformation as it refines by default in 
phenix.refine and keep occupancy of water (the one that is coupled with 
C, qHOH) fixed to some value. Then re-set qHOH = 1-qC and repeat 
refinement again (do not refine qHOH, keep it fixed). Since by default 
phenix.refine will refine partial occupancies, make sure you use 
"remove_selection=resname HOH and resseq 1033" to not refine qHOH but 
keep it at preset value.

Please let me know if you have any questions.


On 6/8/09 2:32 AM, Roeland Boer wrote:
> Dear Pavel,
> Thanks for the reply. I got it working, you were probably right that it 
> was an oversight.
> I have a follow-up question concerning triple conformations: if I have 
> sidechain confs A, B and C and a water molecule sitting in the position 
> of C, can I phenix that it should have the 1-C occupancy (or 1 minus 
> A+B)? I've tried this:
> constrained_group {
>         selection = (chain A and resseq 595 and altloc A) or (resname 
> HOH and resseq 1033)
>         selection = (chain A and resseq 595 and altloc B) or (resname 
> HOH and resseq 1033)
>         selection = (chain A and resseq 595 and altloc C)
> }
> but it gave me an error (obviously)
> Thanks,
> Roeland.
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