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<div class="moz-cite-prefix">Hi Alex,<br>
<br>
thanks for the file - I will have a closer look. Did you mean the
restraint did not work or it worked but you wanted something else?
(I'm just trying to understand if this is a Phenix problem that we
need to fix).<br>
<br>
Pavel<br>
<br>
On 10/18/12 10:30 PM, Alex Theodossis wrote:<br>
</div>
<blockquote
cite="mid:CAKUw-L4UJ22uOv1eLs3zN7goyyEVA1Q-BK2iPgtsKbM4jyhO9g@mail.gmail.com"
type="cite"><font color="#222222" face="arial, sans-serif">Hi
Pavel,</font>
<div><font color="#222222" face="arial, sans-serif"><br>
</font></div>
<div><font color="#222222" face="arial, sans-serif">thanks for the
info. With it I was able to correctly define the
symmetry-related links as per this example:</font></div>
<div><font color="#222222" face="arial, sans-serif"><br>
</font></div>
<div><font color="#222222" face="arial, sans-serif">
<div>refinement.geometry_restraints.edits {</div>
<div> bond {</div>
<div> action = *add</div>
<div>
atom_selection_1 = name ZN and chain C and resname ZN
and resseq 1</div>
<div> atom_selection_2 = name NE2 and chain A and resname
HIS and altid A and resseq 39</div>
<div> symmetry_operation = -x+1,y+1/2,-z+1/2</div>
<div> distance_ideal = 2.030000</div>
<div> sigma = 0.050</div>
<div> }</div>
<div><br>
</div>
<div>Unfortunately, this didn't have the desired result.
Instead, the addition of riding hydrogens fixed the
problem.</div>
<div>I've also attached the relevant fragment of the refined
model as requested.</div>
<div><br>
</div>
<div>Cheers,</div>
<div><br>
</div>
<div>Alex</div>
<div><br>
</div>
<div><br>
</div>
</font><br>
<div class="gmail_quote">On 17 October 2012 13:04, Pavel Afonine
<span dir="ltr"><<a moz-do-not-send="true"
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 bgcolor="#FFFFFF" text="#000000">
<div>Hi Alex,<br>
<br>
Nigel is the best person to reply, so he may provide
more comments. My understanding is that
phenix.metal_coordination command (or whatever the
equivalent click in the GUI is) should account for
symmetry related atoms. If not you can fix it manually.
First create edits file using phenix.metal_coordination
and then add symmetry related bonds as described here:<br>
<br>
<a moz-do-not-send="true"
href="http://www.phenix-online.org/documentation/refinement.htm#anch353"
target="_blank">http://www.phenix-online.org/documentation/refinement.htm#anch353</a><br>
<br>
Also, could you please send me the PDB file or its
portion containing relevant to your question atoms and I
will have a closer look?<br>
<br>
Pavel
<div>
<div><br>
<br>
On 10/16/12 6:33 PM, Alex Theodossis wrote:<br>
</div>
</div>
</div>
<blockquote type="cite">
<div>
<div>
<div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0 0
0 .8ex;border-left:1px #ccc
solid;padding-left:1ex">Dear bb,
<div><br>
</div>
<div>I am trying to refine a Zn ion coordinated
by symmetry related residues. To avoid groups
being pushed away. I have
use phenix.metal_coordination to</div>
<div>generate the necessary link edits. However
only non-symmetry related interactions are
accounted for. Is there a relevant option I
can switch on?</div>
<div>Alternatively, does anyone have an example
of the syntax required to define the necessary
symmetry operations in the elbow.edits file?</div>
<div><br>
</div>
<div>Thanks in advance.</div>
</blockquote>
</div>
<br>
<br>
<fieldset></fieldset>
<br>
</div>
</div>
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</blockquote>
<br>
</div>
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