On Mon, Sep 12, 2011 at 4:50 AM, Simon Kolstoe <span dir="ltr"><<a href="mailto:s.kolstoe@ucl.ac.uk">s.kolstoe@ucl.ac.uk</a>></span> wrote:<br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Dear phenixbb,<br>
<br>
I'm trying to constrain a ligand-metal bond that is continuously getting altered by phenix.refine (my data's only 3.2A). I've added the following restraint but it just doesn't seem to be holding the bond length during refinement.</blockquote>
<div><br></div><div>Could you look in the .geo file to see if the bond restraint was created correctly?</div><div>Look for the atom labels exactly as they appear in the PDB file, e.g. search for exactly</div><div><br></div>
<div><font class="Apple-style-span" face="'courier new', monospace">O1 ROC L � 1</font>�</div><div><br></div><div>If the restraint is in the .geo file but the bond length is not close to the restraint value after refinement there must be some other force pushing the atoms in the wrong direction. I'll need your input files to find out what that is. (I don't need the mtz, but all the rest; send it to me directly.)</div>
<div><br></div><div>Ralf</div><div><br></div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Is there a different way of telling phenix.refine not to alter this distance? (I'm doing it all on the command line & by editing the .def file)<br>
<br>
refinement.geometry_restraints.edits {<br>
�bond {<br>
� �action = *add<br>
� �atom_selection_1 = name CA � and chain X and resname CA and resseq � �1<br>
� �atom_selection_2 = name �O1 �and chain L and resname ROC and resseq � �1<br>
� �distance_ideal = 2.380000<br>
� �sigma = 0.100<br>
�}<br>
}<br>
<br>
Thanks,<br>
<br>
Simon<br>
<br>
---------------------------------------------------------------<br>
Dr Simon Kolstoe<br>
Laboratory for Protein Crystallography<br>
Centre for Amyloidosis & Acute Phase Proteins<br>
UCL Medical School<br>
Rowland Hill Street, London NW3 2PF<br>
<br>
Tel: 020 7433 2765<br>
<a href="http://www.ucl.ac.uk/~rmhasek" target="_blank">http://www.ucl.ac.uk/~rmhasek</a><br>
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</blockquote></div><br>