Dear all

After some fiddling with different software, I managed to get a solution from BALBES in CCP4.

As some suggested, self-rotation indicated only 4 NCS copies in the asu and not 8 based on Matthew's coefficient calculation. In hindsight, the resulting 75 % solvent content could be the cause for the rather poor diffraction.

By using MR Rosetta with the BALBES model, I have something better (R of 32/37 % without adding all the heme ligands yet and some missing atoms not built by AutoBuild).

A request to Phenix developers: When I clicked the Run phenix.refine and Validation buttons in the GUI, it loaded the file overall_best_one.pdb into the GUI which has only one chain. I only noticed this when looking at the 50 % R factor compared to the MR Rosetta log file.

Thanks again.

On Sat, May 2, 2015 at 7:00 PM, Gino Cingolani <Gino.Cingolani@jefferson.edu> wrote:
always check k=180 (2-fold ncs) in addition to whatever high symmetry ncs-axis you think is in your data (e.g. k=45, etc).
There's no guarantee it will work. It's an experimental approach to attempt for difficult MR cases.

******************************************************************************
Gino Cingolani, Ph.D.
Professor
Thomas Jefferson University
Dept. of Biochemistry & Molecular Biology
233 South 10th Street - Room 826
Philadelphia PA 19107
Tel: (215) 503 4573
Website:  http://www.cingolanilab.org
******************************************************************************
"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@phenix-online.org <phenixbb-bounces@phenix-online.org> on behalf of Engin Özkan <eozkan@uchicago.edu>
Sent: Saturday, May 02, 2015 1:09 PM
To: phenixbb@phenix-online.org
Subject: Re: [phenixbb] Molecular replacement at low resolution

On 5/2/15 11:18 AM, Gino Cingolani wrote:
> If you don't see anything at k=45, then you don't have 8 copies in the
> asu.
While checking self rotation functions is a great idea, I would shy away
from such categorical assertions as self rotation functions are not
always cleanly interpretable (despite GLRF, which is my favorite as
well), and an eight-fold NCS might not be due to an eight-fold rotation:
you can have eight molecules with different arrangements (such as two C4
"tetramers") as well as with improper NCS, or through translational NCS
as well.

Engin
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