<div><div>Here is an example:</div><div><br></div><div>refinement.geometry_restraints.edits {</div><div> bond {</div><div> action = *add delete change</div><div> atom_selection_1 = chain A and resname HEM and resid 154 and name FE</div>
<div> atom_selection_2 = chain A and resname MTO and resid 155 and name O</div><div> symmetry_operation = -x,y,-z</div><div> distance_ideal = 2.2</div><div> sigma = 0.01</div><div> }</div></div><div>}</div><div>
<br></div>To get the symmetry_operation, you can either use Coot (turn on drawing on symmetry copies, then click on the copy and look for the symmetry operation in the status bar), or run this command:<div><br></div><div>
iotbx.show_distances your.pdb > all_distances</div><div><br></div><div>This will give you a long all_distances file, but if you look for "sym=" hopefully there will only be a few matches.</div><div><br></div>
<div>Ralf</div><div><br></div><div> <br><div class="gmail_quote">On Thu, Jan 26, 2012 at 11:28 AM, Eike Schulz <span dir="ltr"><<a href="mailto:eike.schulz@embl.de">eike.schulz@embl.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word"><div><div>Dear phenixbb,</div><div><br></div><div>I am sure this is a trivial problem encountered before and that there is a solution to it – however, I was unfortunately not able to solve it myself or with the help of the online documentation.</div>
<div><br></div><div>The problem:</div><div>In one of my structures a nucleic acid chain extends over several symmetry mates. How can I create and refine a bond (in my case 5'-phosphate to 3'-end ) to that symmetry mate? </div>
<div><br></div><div>Many thanks in advance</div><span class="HOEnZb"><font color="#888888"><div><br></div><div>Eike</div></font></span></div></div>
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