[phenixbb] Occupancy refinement issue

AFL alnyds at gmail.com
Fri Oct 7 01:51:53 PDT 2011


Dear All,

  I would like to refine the occupancy of _all_ components together for 
the following system:
- free LYS (chain A and resname LYS)
- PLP-LYS complex (chain A and resname LLP)
- PLP-GLU complex (chian D and resname PPE)

  The LYS and LLP are defined as alternative conformations.

  What I've tried so far is:
- just phenix.refine without any additional constraints and the result 
is occupancy refinement of LYS vs. LLP and separately refined PPE.
- constrained_group {
     selection = chain A and resseq 90 # position of LYS, LLP
     selection = chain C and resseq 1  # PPE
   }
   Result is occupancy refinement of LYS+LLP vs. PPE and total mess in 
the active site (=ligands moved to new positions far away from where 
they should be).
- constrained_group {
     selection = chain A and resname LYS # ALYS, BLLP doesn't work
     selection = chain A and resname LLP
     selection = chain C and resname PPE
   }
  Results in occupancy refinement of LYS vs. PPE and the LLP occupancy 
is set to 0.00.

  So, the big question is:
- is what I'm trying to do doable at all?
- what would be the right way to do it?

  I will appreciate all and any suggestions on how to proceed.

Regards, Andrzej Lyskowski

-- 
  alnyds at gmail.com 		e-mail home


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