[phenixbb] fixing geometry for deposition
rdey at usc.edu
Tue Nov 17 12:02:18 PST 2009
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?
----- 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
> it got distorted during refinement at 2.9A resolution, and
> therefore I
> would suggest re-running phenix.refine using all the restraints
> 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
> 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)".
> 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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