<div dir="ltr"><div><div><div><div><div>Dear all<br><br>After some fiddling with different
software, I managed to get a solution from BALBES in CCP4.<br></div><br></div>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.<br><br></div>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).<br><br></div>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.<br><br></div>Thanks again.<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Sat, May 2, 2015 at 7:00 PM, Gino Cingolani <span dir="ltr"><<a href="mailto:Gino.Cingolani@jefferson.edu" target="_blank">Gino.Cingolani@jefferson.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">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).<br>
There's no guarantee it will work. It's an experimental approach to attempt for difficult MR cases.<br>
<span class=""><br>
******************************************************************************<br>
Gino Cingolani, Ph.D.<br>
Professor<br>
Thomas Jefferson University<br>
Dept. of Biochemistry & Molecular Biology<br>
233 South 10th Street - Room 826<br>
Philadelphia PA 19107<br>
Tel: <a href="tel:%28215%29%20503%204573" value="+12155034573">(215) 503 4573</a><br>
Website: <a href="http://www.cingolanilab.org" target="_blank">http://www.cingolanilab.org</a><br>
******************************************************************************<br>
"Nati non foste per viver come bruti, ma per seguir virtute e canoscenza"<br>
("You were not born to live like brutes, but to follow virtue and knowledge")<br>
Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120)<br>
<br>
<br>
</span>________________________________________<br>
From: <a href="mailto:phenixbb-bounces@phenix-online.org">phenixbb-bounces@phenix-online.org</a> <<a href="mailto:phenixbb-bounces@phenix-online.org">phenixbb-bounces@phenix-online.org</a>> on behalf of Engin Özkan <<a href="mailto:eozkan@uchicago.edu">eozkan@uchicago.edu</a>><br>
Sent: Saturday, May 02, 2015 1:09 PM<br>
To: <a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
<span class="im HOEnZb">Subject: Re: [phenixbb] Molecular replacement at low resolution<br>
<br>
</span><div class="HOEnZb"><div class="h5">On 5/2/15 11:18 AM, Gino Cingolani wrote:<br>
> If you don't see anything at k=45, then you don't have 8 copies in the<br>
> asu.<br>
While checking self rotation functions is a great idea, I would shy away<br>
from such categorical assertions as self rotation functions are not<br>
always cleanly interpretable (despite GLRF, which is my favorite as<br>
well), and an eight-fold NCS might not be due to an eight-fold rotation:<br>
you can have eight molecules with different arrangements (such as two C4<br>
"tetramers") as well as with improper NCS, or through translational NCS<br>
as well.<br>
<br>
Engin<br>
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