[phenixbb] Molecular replacement at low resolution

[mohamed noor]

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 at 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 at phenix-online.org <
> phenixbb-bounces at phenix-online.org> on behalf of Engin Özkan <
> eozkan at uchicago.edu>
> Sent: Saturday, May 02, 2015 1:09 PM
> To: phenixbb at 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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