[phenixbb] Alternative Conformation, Restraints

Moritz Machelett moritz.machelett at bph.rub.de
Mon Oct 14 04:58:24 PDT 2013

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: 
Are there any news/updates on this matter?

Any help appreciated!

Moritz M. Machelett
Ruhr University Bochum
Protein Crystallography, Department of Biophysics, ND04/396
44780 Bochum
Tel: +49-(0)234/32-25754

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20131014/7fee36dd/attachment.htm>

More information about the phenixbb mailing list