[phenixbb] handling of alternate conformations
ulrich.baumann at ibc.unibe.ch
Mon Jul 16 07:11:13 PDT 2007
Dear Phenix experts,
we encounter the following "problem" when trying to refine alternating
we have a complex with 4 chemically different polypeptide chains in the
asymmetric unit, composition A3B3CD. For chains C and D we see additional
density, which appears to belong to three alternating conformations which
can be thought as rigid-body motions (for the whole chains C and D, let's
call these conformers 1,2 and 3, but we label them conventionally in the
file with the prefix A,B,and C) with roughly estimated occupancies of
about 0.3, 0.3 and 0.4 (we can really see most of them). A and B have no
visible alternating conformations (occupancies set to 1.0). From the atom
count it appears that phenix reads in three conformers called A,B and C
with A: A3B3C(1)D(1), B: A3B3C(2)D(2) and C: A3B3C(3)D(3).
Phenix.refine says it has these 3 conformers:
conformer A A:2700 atoms,
conformer B:2700 atoms, common with A 2100,
conformer C:2700 atoms, common with A 2100, common with B 2100.
Refinement yields an R/Rfree of about 0.210/0.325.
If we treat the three conformers of polypeptide chains C and D as
independent chains with occupancy each 1.0 (this is possible 'cos there
are no repulsive contacts between them, fortunately), we get R/Rfree of
0.243/0.291 and phenix applies NCS restraints to all chains.
The resolution is about 2.9 A. We use phenix.refine from the CCI_APPS,
version 2007-03-26-1903, SUSE Linux.
My questions is: is the difference due to the lack of NCS between
conformers or are the occupancies mistreated somwhow? I am asking because
I would not consider the whole A3B3C(x)D(x) particle as a conformer but
only chains C and D ......
Is there a possibility to apply NCS restraints to conformers?
Many thanks in advance,
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