[phenixbb] segmented rigid body refinement

Gino Cingolani Gino.Cingolani at jefferson.edu
Thu Jul 12 09:16:45 PDT 2012

Hi all,
I'm refining a large oligomeric structure at low res (~6A).
I'd like to define groups to use for 'segmented rigid body refinement'. 
Is there any rational way to define 'segments'? 
My macromolecule is already an oligomer on its own, so, intuitively, 
each protomer is a segment. 



Gino Cingolani, Ph.D.
Associate Professor
Thomas Jefferson University
Dept. of Biochemistry & Molecular Biology
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E-mail:   gino.cingolani at jefferson.edu
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"Nati non foste per viver come bruti, ma per seguir virtute e canoscenza"
("You were not born to live like brutes, but to follow virtue and knowledge") Dante,
The Divine Comedy (Inferno,  XXVI, vv. 119-120)

From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Nathaniel Echols [nechols at lbl.gov]
Sent: Thursday, July 12, 2012 7:44 AM
To: PHENIX user mailing list
Subject: Re: [phenixbb] RFZ is higher than TFZ

On Thu, Jul 12, 2012 at 12:38 AM, 周文昌 <wenchangyu2006 at gmail.com> wrote:
> I had one problem using phaser-MR to solve my structure. Phaser-MR gives me
> one solution with TFZ=15.4 and LLG=165 which seems to be promising but
> phenix.refine does not give me a low R values (0.4884/0.5424). I went back
> and checked the solution from phaser-MR, I found RFZ=18.8, higher than TFZ.
> Does anyone think this is a problem to solve my structure?
> The space group is C121, I believe there are 4 copies of my search model in
> ASU.

What is the resolution, and what is the sequence identity of the search model?

I don't know whether the high RFZ means anything, but the first thing
I would check is whether the packing of the MR solution makes sense;
Phaser will do a good job preventing molecules from overlapping
(unless you changed it to use much less conservative criteria), but it
won't guarantee that the molecules pack into a nice continuous
lattice.  If there are big gaps, it may not be a real solution.

I think we need to add an entire FAQ page for high R-factors.
However, there are an increasing number of tools and/or tricks in
Phenix to deal with problems like this - in approximate order of

- run phenix.refine for more cycles - at least 20.  See this paper for
an example of why this can be important:
- use phenix.morph_model (refer to previously mentioned paper)
- use phenix.den_refine (or DEN in CNS)
- use MR-Rosetta

Also, if you're willing to share your data with us, we're collecting
difficult-to-refine structures for benchmarking new methods.  (It will
of course be kept confidential.)

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