On Sat, Jul 30, 2011 at 11:35 AM, Tatyana Sysoeva <span dir="ltr"><<a href="mailto:tatyanasysoeva@gmail.com">tatyanasysoeva@gmail.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;">
I am almost done repeating fix-rotamers run. First time it gave a way
worse validation results then before running phenix without
fix_rotamers=true.<br></blockquote><div><br></div><div>This method behaves very poorly at low resolution - I ran some tests recently on a variety of 3.0-4.5A structures solved by molecular replacement, and while the rotamer fitting usually decreased the R-factor, it always made the clashscore much worse. �I wouldn't bother using it if you have worse than 3.0A data.</div>
<div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><p style="text-align:justify"><span style="font-size:12pt">Model pdb contained the model
identical to the control run but with added H atoms. I have not add H to the
ADP molecules since I did not know how to write a correct CIF file for it.</span></p></blockquote><div><br></div><div>If you use phenix.ready_set, it will handle the ADP molecules.</div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<p style="text-align:justify"><span class="Apple-style-span" style="font-size: 16px; ">Interestingly in previous release
version the same refinement runs produced:</span></p>
<p style="text-align:justify"><span style="font-size:12pt">without H clashscore = 77.580195/cbeta
=8</span></p>
<span style="font-size:12pt">with H clashscore = 119.729960/cbeta=330</span></blockquote><div><br></div><div>We increased the weight on the nonbonded restraints 5x in the last few releases - this always improves the clashscore and Ramachandran statistics at low resolution, although it doesn't change the R-factors very much. �Still, 12% is an awful lot of Ramachandran outliers, even at that resolution. �If you're willing to experiment a little, try adding "ncs.type=torsion" to the parameters (without hydrogens) and let us know what happens.</div>
<div><br></div><div>-Nat</div></div>