[phenixbb] fixing geometry for deposition

[Raja Dey]

Hi Pavel,
              I used the following commands at the last stage of refinement:

phenix.refine 1205A-p21212.mtz nov138_001.pdb simulated_annealing=false ncs_groups.params main.ncs=true ncs.find_automatically=false refinement.ncs.excessive_distance_limit=None main.bulk_solvent_and_scale=false strategy=rigid_body+individual_sites xray_data.high_resolution=2.9 refinement.main.number_of_macro_cycles=1 output.write_maps=true output.prefix=nov139 --overwrite

Regarding amino acids phy, psy..... I tried real space refinement/regularization in coot, but getting the same list of amino acids again and again in the pdb validation summary letter. I also tried mutation on its own to get the ideal geometry, still got the same result.

Did I do anything wrong?


Raja 

----- Original Message -----
From: Pavel Afonine <PAfonine at lbl.gov>
Date: Tuesday, November 17, 2009 11:50 am
Subject: Re: [phenixbb] fixing geometry for deposition
To: PHENIX user mailing list <phenixbb at phenix-online.org>

> 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...
> 
> Pavel.
> 
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