On Tue, Jun 22, 2010 at 2:21 PM, Scott Classen <span dir="ltr"><<a href="mailto:sclassen@lbl.gov">sclassen@lbl.gov</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;">
Hello friendly Phenix developers,<br>
<br>
According to the CHANGES for phenix.refine 1.6.2-432 there is a new feature:<br>
<br>
"hydrogen-bond restraints for Watson-Crick base pairs"<br>
<br>
How do I use this? I couldn't find any documentation... or is it automagic?<br></blockquote><div><br></div><div>Automagic, I hope. �Start with "main.secondary_structure_restraints=True", and it will attempt to find existing base pairs by analyzing hydrogen bonds. �If your geometry is still a little screwy, the parameter syntax is like this:</div>
<div><br></div><div>refinement.secondary_structure.nucleic_acids {</div><div>��base_pair {</div><div>�� �base1 = chain "A" and resseq 1</div><div>�� �base2 = chain "B" and resseq 10</div><div>��}</div>
<div>}</div><div><br></div><div>One piece of advice: make sure your structure has either all hydrogen atoms where they should be, or none at all - if you're missing any, the secondary structure restraints will probably break. �The automatic mechanism will also restrain protein helices and sheets, but you can easily turn this off (restrain_helices=False restrain_sheets=False). �It will probably be necessary to fiddle with the sigma and slack parameters for hydrogen bonds; it isn't clear yet how much these need to be tuned for individual structures, but the defaults don't always work best for all structures.</div>
<div><br></div><div>I am working on a brief sort-of-article on the secondary structure restraints, which has more information about the general mechanism (currently more focused on proteins, which is perhaps a defect). �I'll send you a copy of the current draft. �(A modified version of this will eventually become the official documentation.)</div>
<div><div><br></div><div>-Nat</div></div></div>