[phenixbb] fixing geometry for deposition

Raja Dey rdey at usc.edu
Tue Nov 17 12:07:32 PST 2009

I attached the summary letter.
Thanks for your time.


----- Original Message -----
From: "Ralf W. Grosse-Kunstleve" <rwgk at cci.lbl.gov>
Date: Tuesday, November 17, 2009 11:48 am
Subject: Re: [phenixbb] fixing geometry for deposition
To: phenixbb at phenix-online.org

> >                      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?
> Ralf
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