[phenixbb] Alternative Conformation, Restraints

Pavel Afonine pafonine at lbl.gov
Sun Oct 27 09:40:37 PDT 2013

Hi Moritz,

sorry for delayed reply - I was away with limited email access.

Please send me (to my email address) PDB model and data files (as well 
as ligand cif files, if any available) and also indicate residues in 
problem, and I will check to see what's going on.

 From reading your email it seems the problem may be with PDB formatting 
(like having TER record between alternate conformers, for instance), but 
could well be something else.

Regarding turning off non-bonded restraints: could you please explain 
what exactly and why you are trying to do?


On 10/14/13 4:58 AM, Moritz Machelett wrote:
> Hello everyone,
> I am in the final rounds of refining my protein at high resolution and
> currently trying to model an alternative conformation of a Chl
> /a/-phytol chain. I inserted a second phytol chain with coot - worked
> out well so far (alternate chain identifiers A and B for both phytol
> chains). After using phenix.refine, however, the occupancy of the second
> phytol chain was refined to 0. When splitting the whole Chl molecule the
> occupancy refines to sensible values (0.34 and 0.66). We would prefer to
> only model the phytol chain in alternate conformation as the macrocycle
> superpose perfectly. Any suggestions regarding the occupancy problem?
> Another issue concerns restraints. We tried to turn of specific
> nonbonded restraints and found a phenixbb message from 2007:
> http://www.phenix-online.org/pipermail/phenixbb/2007-September/011734.html
> Are there any news/updates on this matter?
> Any help appreciated!
> Thanks,
> Moritz
> --
> Moritz M. Machelett
> Ruhr University Bochum
> Protein Crystallography, Department of Biophysics, ND04/396
> 44780 Bochum
> Tel: +49-(0)234/32-25754
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