On Wed, Apr 7, 2010 at 4:38 PM, r n <span dir="ltr"><<a href="mailto:ramme29@yahoo.com">ramme29@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:12pt"><div style="font-family:arial,helvetica,sans-serif;font-size:12pt">I wanted to do low resolution rigid body refinement with secondary structural restrain. I have not seen<br>
any command or information in the phenix document?<br></div></div></div></blockquote><div><br></div><div>Okay, finally writing documentation now. �Sorry! �There isn't actually a method for combining rigid body refinement with secondary structure information yet; it would probably be a day or two of work for Pavel or me. �However, the "morph" option on AutoBuild may do a better job at moving pieces of that size into place. �(And there are probably other programs which I haven't used that do something similar.)</div>
<div><br></div><div>You can use the secondary structure restraints with simple coordinate refinement (strategy individual_sites), by adding "main.secondary_structure_restraints=True" to the command-line (there is a corresponding button in the GUI, but only if you have the alpha-test mode turned on). �Everything else is (in theory) automatic, but if you aren't using hydrogens, add "h_bond_restraints.substitute_n_for_h=True" as well, just to be safe.</div>
<div><br></div><div>-Nat</div></div>