[phenixbb] fixing geometry for deposition

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Tue Nov 17 11:48:49 PST 2009

>                      pdb validation summary letter gives a list
> of covalent bond angles greater than 6 times standard deviation for
> dna part of my molecule. I am wondering if someone can tell how to
> fix that. I used PHENIX to refine my molecule. I did not use any
> restraints for the dna part.

Do you mean hydrogen-bond restraints? -- At 2.9A the structure would
probably be completely distorted if you didn't have any restraints.
The 6 times standard deviation should not happen if we use the same
restraints as the pdb is expecting. If you send me (off-list) the
inputs and the pdb summary letter we'll take a closer look.

> Also a few amino acids are listed for which phy and psy fall outside
> Ramachandran plot. I like to know what is the best way to fix these
> phy, psy angles.

A few outliers are expected. Did you look at them in coot?


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