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Hi, <br>
<br>
I have the similar problem when I am working on refining my low resolution model (3.5 Ang).<br>
<br>
One component of my protein complex represents a beta-sandwish structure, and the conecting loops between beta-strands are disordered.<br>
After refinement, the beta-sheets were disrupted.<br>What do you suggest about this problem.<br><br><br>PC<br><br><hr id="stopSpelling">Date: Sun, 10 Oct 2010 16:48:57 -0700<br>From: pafonine@lbl.gov<br>To: qunwan1@gmail.com; phenixbb@phenix-online.org<br>Subject: Re: [phenixbb] about low resolution refinement<br><br>
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Hello,<br>
<br>
<blockquote cite="mid:AANLkTim=2NW727G5WvKAKMRez=TwoX+jPf5y-hWk7kO+@mail.gmail.com">I am refining a low resolution data. According to
sigma vs. resolution, my resolution is 4.7A. </blockquote>
<br>
not sure what is "sigma vs. resolution" but hope you made the right
decision.<br>
<br>
<blockquote cite="mid:AANLkTim=2NW727G5WvKAKMRez=TwoX+jPf5y-hWk7kO+@mail.gmail.com">Because there are four identical molecular per
asymetric unit, I can use positional refinement. There are about
65% alpha-helices in the structure, so I want to use secondary
structure restrain. Does phenix has this restrain in the
refinement?<br>
</blockquote>
<br>
Sorry for missing documentation on this subject.<br>
<br>
First of all, get the latest version of PHENIX (the one you have is
very old):<br>
<br>
<a class="ecxmoz-txt-link-freetext" href="http://www.phenix-online.org/download/nightly_builds.cgi" target="_blank">http://www.phenix-online.org/download/nightly_builds.cgi</a><br>
<br>
Then (once you have the latest), yes, you can use secondary
structure restraints. <br>
<br>
phenix.refine model.pdb data.hkl
main.secondary_structure_restraints=true<br>
<span class="ecxApple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Times; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; font-size: medium;"><span class="ecxApple-style-span" style="font-family: verdana,helvetica,arial,sans-serif; font-size: 14px;"><br>
so phenix.refine automatically determines secondary structure
and applies the restrains. Note, GIGO principle applies, that is
if your input model is distorted then it's unlikely that the
procedure will figure out the secondary structure correctly.<br>
<br>
To make it a less black-box, you can run<br>
<br>
phenix.secondary_structure_restraints model.pdb >
ss_restraints.params<br>
<br>
and then check (and edit if necessary) the </span></span><span class="ecxApple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Times; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; font-size: medium;"><span class="ecxApple-style-span" style="font-family: verdana,helvetica,arial,sans-serif; font-size: 14px;">ss_restraints.params file, and then run
phenix.refine as following:<br>
<br>
</span></span>phenix.refine model.pdb data.hkl
main.secondary_structure_restraints=true <span class="ecxApple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Times; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; font-size: medium;"><span class="ecxApple-style-span" style="font-family: verdana,helvetica,arial,sans-serif; font-size: 14px;">ss_restraints.params<br>
<br>
I hope Nat comments more if I missed something.<br>
<br>
Let me know if you have any other questions.<br>
<br>
Good luck!<br>
Pavel.<br>
<br>
<br>
<br>
</span></span>
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