<div dir="ltr">Ed<div><br></div><div style>You can use an edits. You can use the slack option to create a flat bottomed well which will allow the bond to be any value of distance_ideal plus/minus slack. The sigma curve starts at the border of the slack region.</div>
<div style><br></div><div style>I have given the example from the on-line docs below.</div><div style><br></div><div style>Cheers</div><div style><br></div><div style>Nigel</div><div style><br></div><div style><pre class="" style="color:rgb(0,0,0)">
refinement.geometry_restraints.edits {
zn_selection = chain X and resname ZN and resid 200 and name ZN
his117_selection = chain X and resname HIS and resid 117 and name NE2
asp130_selection = chain X and resname ASP and resid 130 and name OD1
bond {
action = *add
atom_selection_1 = $zn_selection
atom_selection_2 = $his117_selection
symmetry_operation = None
distance_ideal = 2.1
sigma = 0.02
slack = None
}</pre></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, Apr 19, 2013 at 1:08 PM, Edward A. Berry <span dir="ltr"><<a href="mailto:BerryE@upstate.edu" target="_blank">BerryE@upstate.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">I have a phenix-specific question and a general chemistry question.<br>
In a ligand-bound structure, S in an aromatic ring (substituted thiophene)<br>
may be H-bonding NH1 of arginine guanidino group.<br>
The general question is whether thiophene S can act as H-bond acceptor<br>
(assuming one lone pair is in the aromatic pi system for a total of 6 e,<br>
the other lone pair is available as H-bond acceptor?).<br>
<br>
The phenix-specific question involves whether non-bonded interactions<br>
will push the atoms apart during refinement, and how to turn off the<br>
nonbonded interaction between these two atoms to allow the xray data<br>
to determine the position.<br>
Under geometry_restraints.edits I define a bond, but give a very<br>
large sigma of 1A.<br>
Will this effectively remove non-bonded interactions between these<br>
two atoms?<br>
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</blockquote></div><br><br clear="all"><div><br></div>-- <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>
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