[phenixbb] Refine three alternate conformations of residues and two loop confirmations.

Pavel Afonine pafonine at lbl.gov
Mon Oct 13 09:16:47 PDT 2014


Hi Amit,

there is no limit on number of conformations. Usually it requires 
looking at the files in order to make a meaningful suggestion. If you 
send me files off mailing list and indicate residues in question I will 
be happy to have a closer look.

General guidance for occupancy refinement is here:
  http://phenix-online.org/documentation/reference/refinement.html#occupancy-refinement

Pavel

On 10/13/14 9:07 AM, AMIT wrote:
> Hi All,
>          I am unable to refine three alternate conformations of a 
> residue provided in PDB file prefixed before resname as A,B and C in 
> Phenix dev-1370. When I make it two alternate conformations it runs OK.
>
> Also I am not able to refine two loop confirmations, the refinement 
> somehow puts both in the major 2Fo-Fc map peak and makes the almost 
> same, even though the starting loop has different trace.Turning off 
> siulated annealing or making temp. lower or just doing 1 cycle is not 
> doing any good.
>
> Any suggestions will be helpful.
>
> Thanks,
> Amit.
>
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