<html><body><div style="color:#000; background-color:#fff; font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:10pt">Hi Len,<br>Can't you re-run rigid body in Phenix and feed it directly to SA?<br>Just trying to stay involved, feel free to ignore me....<br>:)<br><div><span><br></span></div><div style="display: block;" class="yahoo_quoted"> <br> <br> <div style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 10pt;"> <div style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 12pt;"> <div dir="ltr"> <font face="Arial" size="2"> On Thursday, January 23, 2014 3:59 PM, Pavel Afonine <pafonine@lbl.gov> wrote:<br> </font> </div> <div class="y_msg_container"><div id="yiv3884272306"><div>
Hello,<br clear="none">
<br clear="none">
this means the PDB file that you gave to phenix.refine contains
atoms that perfectly (within 0.0001) overlap. If that's what you
want, then just follow what phenix.refine suggests to keep going (I
think it prints out a keyword that disables this error message).
Otherwise edit PDB file and run refinement again.<br clear="none">
<br clear="none">
If this does not help please send me PDB file.<br clear="none">
<br clear="none">
Pavel<br clear="none">
<br clear="none">
<div class="yiv3884272306yqt7592857696" id="yiv3884272306yqt33423"><div class="yiv3884272306moz-cite-prefix">On 1/23/14, 12:31 PM, Leonard Thomas
wrote:<br clear="none">
</div>
<blockquote type="cite">Hello All,
<div><br clear="none">
</div>
<div>We are trying to refine a complex that was solved using
Phaser. We have run a round of rigid body refinement using
Refmac and now want to run a simulated annealing run in Phenix.
Visually the complex looks pretty. The resolution we currently
are at is 3.6 A. When we go to run phenix.refine the program
quits with a Number of non-bonded interactions < 0.0001
error. Is there a way to loosen this up a bit or get around it
or should we go about this in a different way? </div>
<div><br clear="none">
</div>
<div>Best Regard,</div>
<div><br clear="none">
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<div>Leonard Thomas, Ph.D.</div>
<div>Macromolecular Crystallography
Laboratory Manager</div>
<div>University of Oklahoma</div>
<div>Department of Chemistry and
Biochemistry</div>
<div>Stephenson Life Sciences Research
Center</div>
<div>101 Stephenson Parkway</div>
<div>Norman, OK 73019-5251</div>
</div>
</div>
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<span class="yiv3884272306Apple-style-span" style="font-size:12px;">Office: (405)325-1126</span>
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</blockquote></div>
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