[phenixbb] handling of alternate conformations

Pavel Afonine PAfonine at lbl.gov
Mon Jul 16 14:53:24 PDT 2007

Hi Ulrich,

> My first question is whether NCS constraints are also applied to alternate  
> conformations.

1) phenix.refine does not have NCS constraints but it has only NCS 
2) I presume it will use whatever you specify in your selections for NCS 
groups (Ralf -- could you confirm this please?). If you include atoms in 
alternative conformation -- they will be used in NCS restrains.

> My second question concerns the atom count of the conformers, where the  
> parts with non-alternating conformations seem to be included as well

If I correctly understand your question, this is how alternative 
conformations are handled. Internally, for each conformer phenix.refine 
generates a separate chain. For example, if an atom in chain has 2 
alternative conformations, then phenix.refine will create three 
chains-duplicates each containing unique conformation (one for main 
conformation and two for two alternative ones); each such created chain 
is called conformer.


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