<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:"arial", "helvetica", sans-serif;font-size:10pt"><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 <nwmoriarty@lbl.gov><br><b><span style="font-weight: bold;">To:</span></b> PHENIX user mailing list
<phenixbb@phenix-online.org><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><br>
<br><br><div class="gmail_quote">On Thu, Dec 2, 2010 at 12:20 PM, Pavel Afonine <span dir="ltr"><<a rel="nofollow" ymailto="mailto:pafonine@lbl.gov" target="_blank" href="mailto:pafonine@lbl.gov">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 class="h5"><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" target="_blank" href="http://CCI.LBL.gov">CCI.LBL.gov</a><br>
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