ram<div><br></div><div>The sigma value (standard deviation) is exactly what is used to restrict the variance of the bond lengths. Starting with the default value, you can reduce it by a factor of ten (at the most) and the bond should remain closer to the ideal. If not, there may be other things involved. The angle restraints or the density.</div>
<div><br></div><div>Nigel<br><br><div class="gmail_quote">On Thu, Dec 2, 2010 at 1:59 PM, r n <span dir="ltr"><<a href="mailto:ramme29@yahoo.com">ramme29@yahoo.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div><div style="font-family:"><div>Thanks a lot, I did that, when ever I update the coordinates and more cycle of refinement,</div><div>the distance is varies. I tried sigma value in the elbow edits but did not help.</div>
<div><br></div><div>How can I keep the distance constrained for example (2.4 to 2.6A) or more strict 2.6 to 2.65?<br></div><div><br></div><div>Thanks</div><div><br></div><div><br></div><div>ram</div><div style="font-family:arial, helvetica, sans-serif;font-size:10pt">
<br><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><font size="2" face="Tahoma"><hr size="1"><b><span style="font-weight:bold">From:</span></b> Nigel Moriarty <<a href="mailto:nwmoriarty@lbl.gov" target="_blank">nwmoriarty@lbl.gov</a>><br>
<b><span style="font-weight:bold">To:</span></b> PHENIX user mailing list
<<a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a>><br><b><span style="font-weight:bold">Sent:</span></b> Thu, December 2, 2010 2:55:22 PM<br><b><span style="font-weight:bold">Subject:</span></b> Re: [phenixbb] distance constrain in phenix<br>
</font><div><div></div><div class="h5"><br>
<br><br><div class="gmail_quote">On Thu, Dec 2, 2010 at 12:20 PM, Pavel Afonine <span dir="ltr"><<a rel="nofollow" href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
Hi,<br>
<br>
step 1:<br>
Run<br>
phenix.metal_coordination model.pdb<br>
this will create a file defining the protein-metal restraints.<br>
<br>
step 2: <br>
Look at this file and make sure the defined restraints match your
expectations.<br></div></blockquote><div><br></div><div>Take particular note of the angles. You may wish to delete them for the first few rounds of refinement. </div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<br>
step 3:<br>
Use this file in phenix.refine runs.<br><font color="#888888">
<br>
Pavel.</font><div><div><br>
<br>
<br>
On 12/2/10 12:07 PM, r n wrote:
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<div>Hi<br>
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<div>I would like to do distance
restrain refinement for metal
coordination.</div>
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<div>How can I do metal - protein
strict distance restrain
refinement in phenix? </div>
<div><br>
</div>
<div>Thanks</div>
<div>ram</div>
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<br></blockquote></div><br><br clear="all"><br>-- <br>Nigel W. Moriarty<br>Building 64R0246B, Physical Biosciences Division<br>Lawrence Berkeley National Laboratory<br>Berkeley, CA 94720-8235<br>Phone : 510-486-5709 Email : NWMoriarty@LBL.gov<br>
Fax : 510-486-5909 Web : <a rel="nofollow" href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a><br>
</div></div></div></div>
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<br></blockquote></div><br><br clear="all"><br>-- <br>Nigel W. Moriarty<br>Building 64R0246B, Physical Biosciences Division<br>Lawrence Berkeley National Laboratory<br>Berkeley, CA 94720-8235<br>Phone : 510-486-5709 Email : NWMoriarty@LBL.gov<br>
Fax : 510-486-5909 Web : <a href="http://CCI.LBL.gov">CCI.LBL.gov</a><br>
</div>