If you use restraints to fix outliers, I strongly suggest to refine to convergence without
restraints after they are "fixed". If some outliers return, and "% favored"
decreases, so be it.
For one thing, depositing a structure with dihedrals restrained gives an unfair
impression of higher quality compared to similar structures whose "% favored"
actually represents the ability of the data to give the correct conformation.
More importantly, you may actually be making a worse model of those (~0.2%?) of residues that are
real outliers, and (~5%?) that are really "allowed" and not "favored".
At least that's how it used to be:
On 12/20/2006 10:34 PM, Gerard DVD Kleywegt wrote:
you have to ask yourself if you really, really, really want to do that. and if
the answer is 'yes' you have to ask yourself again
the reason is that the conformational torsion angles are eminently suited for
validation purposes, but only when they are unrestrained. in other words, once
you restrain phi and psi, you can't use ramachandran plots any longer (well,
you can, but they are useless as validation tools)
On 02/25/2015 12:21 PM, Robbie Joosten wrote:
Hi Michael,
This depends a bit on how bad your backbone torsion angles are and why.
Refining with good restraint weights and flipping the odd peptide can help a
lot. If you have really low resolution you might need specific restraints. You
can try the PDB_REDO webserver at http://xtal.nki.nl/PDB_REDO which will
optimise the restraint weights for REFMAC and flip peptides if the density and
the Ramachandran plot show that this is needed. You can also try adding
hydrogen bond restrains from ProSMART to help the Ramachandran plot in regions
that have reasonable secondary structure. This works quite well at resolutions
lower than ~3A.
HTH,
Robbie
-----Original Message-----
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Michael Murphy
Sent: Wednesday, February 25, 2015 18:09
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] adjusting bad Ramachandran angles
Does anyone know of a way to adjust Ramachandran angles so that they fall
within the preferred range? Either in Coot or possibly some online server? I
have been trying to do it manually without much success, I was wondering
whether there might another way to do it. -Thanks
