[phenixbb] fixing geometry for deposition

Pavel Afonine PAfonine at lbl.gov
Tue Nov 17 11:50:24 PST 2009

Hi Raja,

>                      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.

did you completely turn off all the geometry restraints for that 
selected part of your structure? If so, then it is not surprising that 
it got distorted during refinement at 2.9A resolution, and therefore I 
would suggest re-running phenix.refine using all the restraints that 
phenix.refine normally uses by default.

>                      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.

1) Can't you do it in Coot? (especially when there are only a few such 
outliers, as you say).

2) Try adding riding H atoms and re-run phenix.refine (with and w/o 
weights optimization to see which option gives better results).

3) Try a quick geometry regularization going into trying "2)". Repeat 
the same with and w/o H.

This is a pretty frequent question, so I hope someone someone can tell a 
success story about it...

> Final refined parameters are
> REMARK Start: r_work = 0.3576 r_free = 0.3345 bonds = 0.009 angles = 1.344      
> REMARK Final: r_work = 0.2517 r_free = 0.2845 bonds = 0.008 angles = 1.209      
> at 2.9A resolution

Looks reasonable given the resolution...


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