<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Thanks so much Pavel for the very rapid response! One more thing, it is a disulfide linked DTT so do I do anything special to ensure that all the sulfur atoms (4 in total - two in one unit cell - one each from the cys and dtt and two in the other unit cell) stay in close enough contact for a covalent bond and not move due to non-bonded contact distance restraints?<br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: 'Lucida Grande'; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: 'Lucida Grande'; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">___________________________________________________________</div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Joseph P. Noel, Ph.D.<br>Investigator, Howard Hughes Medical Institute<br>Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics<br>The Salk Institute for Biological Studies<br>10010 North Torrey Pines Road<br>La Jolla, CA 92037 USA<br><br>Phone: (858) 453-4100 extension 1442<br>Cell: (858) 349-4700<br>Fax: (858) 597-0855<br>E-mail: <a href="mailto:noel@salk.edu">noel@salk.edu</a><br><br>Web Site (Salk): <a href="http://www.salk.edu/faculty/faculty_details.php?id=37">http://www.salk.edu/faculty/faculty_details.php?id=37</a><br>Web Site (HHMI): <a href="http://hhmi.org/research/investigators/noel.html">http://hhmi.org/research/investigators/noel.html</a><br>___________________________________________________________<br></div></span></span>
</div>
<br><div><div>On Aug 3, 2010, at 6:05 PM, Pavel Afonine wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">
<div bgcolor="#ffffff" text="#000000">
Hi Joe,<br>
<br>
I think all you need is summarized here:<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.phenix-online.org/pipermail/phenixbb/2009-December/003070.html">http://www.phenix-online.org/pipermail/phenixbb/2009-December/003070.html</a><br>
<br>
Please let us know if you still have any questions.<br>
<br>
ReadySet creates a CIF file wich has nothing to do with the
occupancies, symmetry etc... It just defines the geometry of your
DTT. So, create a CIF file for DTT (if you really need it - I
thought it is standard thing and might be already in the library)
and run the refinement following the tips in the link above.<br>
<br>
Pavel.<br>
<br>
<br>
On 8/3/10 5:54 PM, Joseph Noel wrote:
<blockquote cite="mid:3D85729E-AFB7-46A7-8BC5-DD0851C86B00@salk.edu" type="cite">Hi Phenix Users,
<div><br>
</div>
<div>I have found a beautifully ordered DTT molecule stretching
across a crystallographic two-fold and linking two symmetry
related cysteine side chains. Since part of this molecule sits
on across the two-fold (special position) I will specify the
occupancy as 0.5. I am hoping to get some information on how
easy (or how difficult) it is to specify this arrangement in
Phenix for refinement since it is covalent and sitting across a
crystallographic two-fold (and presumably stabilizing the
lattice). Will ReadySet build the appropriate CIF file if I
build the DTT into the density and give it a 0.5 occupancy?</div>
<div><br>
</div>
<div>Joe<br>
<div>
<span class="Apple-style-span" style="border-collapse: separate; font-family: 'Lucida Grande'; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; "><span class="Apple-style-span" style="border-collapse: separate; font-family: 'Lucida Grande'; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; ">
<div style="word-wrap: break-word;">___________________________________________________________</div>
<div style="word-wrap: break-word;">Joseph P. Noel, Ph.D.<br>
Investigator, Howard Hughes Medical Institute<br>
Professor, The Jack H. Skirball Center for Chemical
Biology and Proteomics<br>
The Salk Institute for Biological Studies<br>
10010 North Torrey Pines Road<br>
La Jolla, CA 92037 USA<br>
<br>
Phone: (858) 453-4100 extension 1442<br>
Cell: (858) 349-4700<br>
Fax: (858) 597-0855<br>
E-mail: <a moz-do-not-send="true" href="mailto:noel@salk.edu">noel@salk.edu</a><br>
<br>
Web Site (Salk): <a moz-do-not-send="true" href="http://www.salk.edu/faculty/faculty_details.php?id=37">http://www.salk.edu/faculty/faculty_details.php?id=37</a><br>
Web Site (HHMI): <a moz-do-not-send="true" href="http://hhmi.org/research/investigators/noel.html">http://hhmi.org/research/investigators/noel.html</a><br>
___________________________________________________________<br>
</div>
</span></span>
</div>
<br>
</div>
<pre wrap=""><fieldset class="mimeAttachmentHeader"></fieldset>
_______________________________________________
phenixbb mailing list
<a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a>
</pre>
</blockquote>
<br>
</div>
</blockquote></div><br></body></html>