[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
restraints.
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.
Pavel.
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