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.
Thanks,
Gino
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Gino Cingolani, Ph.D.
Associate Professor
Thomas Jefferson University
Dept. of Biochemistry & Molecular Biology
233 South 10th Street - Room 826
Philadelphia PA 19107
Office (215) 503 4573
Lab (215) 503 4595
Fax (215) 923 2117
E-mail: [email protected]
Website: http://www.cingolanilab.org
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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)
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From: [email protected] [[email protected]] on behalf of Nathaniel Echols [[email protected]]
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
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 runtime: - run phenix.refine for more cycles - at least 20. See this paper for an example of why this can be important: http://journals.iucr.org/d/issues/2012/07/00/kw5044/index.html - 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.) -Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb