Just a thought, but running the default "phenix.refine" command is going to refine individual atomic coordinates and ADPs, unless you specify otherwise. At 3.3A are you sure you have enough data to model all of these parameters? Even with heavy restraints, i'm not sure individual coordinate refinement is feasible. Perhaps doing a rigid-body refinement of multiple groups with grouped ADPs would yield better results. You could even model in TLS groups.
From what I understand, if you regularize the geometry before refinement as Pavel suggested, the side-chains shouldn't move back to outlier regions, since the side-chains will not be refined in rigid-bodies.
Just a friendly thought :)
Best wishes,
Jason Porta
Graduate Student
Eppley Structural Biology Facility
Dept. Biochemistry & Molecular Biology
University of Nebraska Medical Center
Omaha, NE 68198
(402) 559-5533
-----phenixbb-bounces@phenix-online.org wrote: -----
To: "PHENIX user mailing list" <phenixbb@phenix-online.org>
From: "guanrj@foxmail.com" <guanrj@foxmail.com>
Sent by: phenixbb-bounces@phenix-online.org
Date: 04/14/2010 12:00PM
Subject: Re: [phenixbb] Phenix.refine bonds/angles rmsd
Thank you
very much for your suggestions. I will try all these options and let you
know
the results.
Rongjin
= = = = = = =
= On 2010-04-14 12:03:10 You
wrote = = = = = = = =
Hi
Rongjin,
I am refining another 3.3 A
resolution structure. In coot I manually adjusted the
model
to have >95% residues
in preferred region in ramanchandran plot, but after
refinement
in Phenix only <80% residues in the preferred region and a
lot more in the outlier region.
This was wen I used the default
refinement parameters "phenix.refine mtz_file pdb_file".
R and R_free are 0.22/0.27 in this
case.
you may want to
consider:
- using secondary structure restraints;
- tightening
restraints (using wxc_scale=...);
- using H atoms in refinement;
-
doing some quick geometry regularization before refinement;
- fixing
manually and excluding from refinement certain parts of your
model.
You need to experiment and find empirically which
combination of the above options works in your case. I would appreciate
if you share your experience with this and tell us what worked for your
in the
end.
Pavel.
|
_______________________________________________
phenixbb mailing list
phenixbb@phenix-online.org
http://phenix-online.org/mailman/listinfo/phenixbb