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? Thanks, Pavel 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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