On Mon, Jul 19, 2010 at 6:15 AM, Hermella Woldemdihin <span dir="ltr"><<a href="mailto:hermifi@yahoo.com">hermifi@yahoo.com</a>></span> wrote:<br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div><div style="font-family:arial,helvetica,sans-serif;font-size:10pt"><div>I am new to phenix.refine. I'm using the graphical interface.<br>I hav processed my dfiffraction data and used Phaser MR for molecular replacement.<br>
And I goyt a result: a solution pdb file and the associated mtz file.<br>1. So I use the mtz file from this Phaser MR solution or the original file from my data<br>processing in phenix.refine?<br></div></div></div></blockquote>
<div><br></div><div>The original file. �I think Phaser outputs anisotropy-corrected data, and it may be at reduced resolution depending on how you run it.</div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div><div style="font-family:arial,helvetica,sans-serif;font-size:10pt"><div>2. I have set parameters for phenix.refine like this:<br>Is there other settings for the parameter which I should do for a better result?<br>PDB data: my solution from Phaser MR<br>
XRAY DATA= ????<br>Simulated Annealing=1000<br>Update waters<br>Refine Target weights: Wxc=0.8 Wxu=1.6<br>Cycles=5<br>Fix rotamers<br>Fix bad side chains<br></div>
</div></div></blockquote></div><br><div>Unless you've already run refinement with this dataset and are confident about the weights, I would not set wxc and wxu initially; automatic weight optimization is a better place to start. �Otherwise, which refinement settings are most appropriate depends on the resolution and starting R-free. �As Frederic points out, rigid-body refinement may be a good idea at this stage. �(By the way, you list both "Fix rotamers" and "Fix bad side chains", but these are the same thing - unless I mislabeled something in the GUI...)</div>
<div><br></div><div>-Nat</div>