[phenixbb] about low resolution refinement
Pei-Chun Lin
pclin at hotmail.com
Sat Oct 16 17:15:29 PDT 2010
Hi,
I have the similar problem when I am working on refining my low resolution model (3.5 Ang).
One component of my protein complex represents a beta-sandwish structure, and the conecting loops between beta-strands are disordered.
After refinement, the beta-sheets were disrupted.
What do you suggest about this problem.
PC
Date: Sun, 10 Oct 2010 16:48:57 -0700
From: pafonine at lbl.gov
To: qunwan1 at gmail.com; phenixbb at phenix-online.org
Subject: Re: [phenixbb] about low resolution refinement
Hello,
I am refining a low resolution data. According to
sigma vs. resolution, my resolution is 4.7A.
not sure what is "sigma vs. resolution" but hope you made the right
decision.
Because there are four identical molecular per
asymetric unit, I can use positional refinement. There are about
65% alpha-helices in the structure, so I want to use secondary
structure restrain. Does phenix has this restrain in the
refinement?
Sorry for missing documentation on this subject.
First of all, get the latest version of PHENIX (the one you have is
very old):
http://www.phenix-online.org/download/nightly_builds.cgi
Then (once you have the latest), yes, you can use secondary
structure restraints.
phenix.refine model.pdb data.hkl
main.secondary_structure_restraints=true
so phenix.refine automatically determines secondary structure
and applies the restrains. Note, GIGO principle applies, that is
if your input model is distorted then it's unlikely that the
procedure will figure out the secondary structure correctly.
To make it a less black-box, you can run
phenix.secondary_structure_restraints model.pdb >
ss_restraints.params
and then check (and edit if necessary) the ss_restraints.params file, and then run
phenix.refine as following:
phenix.refine model.pdb data.hkl
main.secondary_structure_restraints=true ss_restraints.params
I hope Nat comments more if I missed something.
Let me know if you have any other questions.
Good luck!
Pavel.
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