[phenixbb] handling of alternate conformations

Ulrich Baumann 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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