[phenixbb] very short peptide bond issue

Luo, Jeffrey [JRDUS] Jluo at its.jnj.com
Tue Aug 23 12:41:03 PDT 2011

Hi Pavel,

I am refining a structure to 1A resolution (which I had asked you about
before). It is nearly complete. However, one peptide bond is very short
(1.2A vs ~1.33A).  From the density, it appears that the two residues
flanking the peptide bond have (at least) two conformations.  I have
tried to model both as a single and double conformers.  In both cases,
PHENIX seems to force the single or both conformers into the average
position, which of course leads to the short apparent peptide bond.  

Can you suggest any way to fix this problem?  If you prefer, I can send
you the models and the data file to have a look.

Thanks a lot.


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