Hi Ralf,<div><br></div><div>Thanks a lot for the fast response.</div><div>I have actually tried setting all occupancies to 0.5 and it didn&#39;t work. Also I could find how to define custom bonds, but I am not clear with how to use symmetry operations and pseudo bonds (I know how to turn on symmetry in coot). Following are the commands I came up with for custom bonds</div>
<div>







<p class="p1">refinement.geometry_restraints.edits {</p>
<p class="p1">bond {</p>
<p class="p1">action  = *add</p>
<p class="p1">atom_selection_1 = chain y and resseq 2 and name N1</p>
<p class="p1">atom_selection_2 = chain y and resseq 2 and name C4</p>
<p class="p1">distance_ideal = 3.0</p>
<p class="p1">sigma = 0.02</p>
<p class="p1">slack = None</p>
<p class="p1">}</p>
<p class="p1">bond {</p>
<p class="p1">action  = *add</p>
<p class="p1">atom_selection_1 = chain y and resseq 2 and name N1</p>
<p class="p1">atom_selection_2 = chain Z and resseq 1 and name TB</p>
<p class="p1">distance_ideal = 2.5</p>
<p class="p1">sigma = 0.02</p>
<p class="p1">slack = None</p>
<p class="p1">}</p>
<p class="p1">}</p></div><div>Also if I want to run refine in GUI can I give these commands as an input file? If so what is the file format I should use?<br><br>Thanks in advance</div><div>Subhani</div><div><br><div class="gmail_quote">
On Mon, Oct 17, 2011 at 2:50 PM, Ralf Grosse-Kunstleve <span dir="ltr">&lt;<a href="mailto:rwgrosse-kunstleve@lbl.gov">rwgrosse-kunstleve@lbl.gov</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div class="gmail_quote"><div class="im"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div>So I left only half of that DPA ligand structure on PDB file and changed the occupancy of N1 and C4 to 1/2 while keeping the occupancy of all other atoms of the half ligand structure at 1.00.</div>

</blockquote><div><br></div></div><div>Keep the occupancy of N1 and C4 as 1.00, then phenix.refine should automatically detect those as special positions and keep them exactly on the two-fold axis.</div><div>The bonds and other restraints to the atoms on special positions will not work automatically. Currently, the only option is to define custom bonds (see phenix.refine docs) with symmetry_operation=x,y,z. You can use Coot to obtain the symmetry operation (turn on drawing of symmetry copies; when clicking atom Coot will show the sym op). Emulate angle and dihedral restraints with pseudo-bonds. Inspect the .geo file to verify that all restraints are correct.</div>

<div><br></div><div>You can also keep all DPA atoms, with all occupancies set to 0.5. Then the restraints will work as usual; probably you don&#39;t have to do anything special. However, the N1 and C4 are allowed to float around the special position. It may be OK though. I think I&#39;d try this option first.</div>

<div><br></div><font color="#888888"><div>Ralf</div><div><br></div></font></div>
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