On Thu, May 20, 2010 at 8:54 AM, John Pascal <span dir="ltr"><<a href="mailto:John.Pascal@mail.jci.tju.edu">John.Pascal@mail.jci.tju.edu</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;">
I would like to restrain the positions of ribose/phosphate atoms of<br>
altloc 'A' to the positions of those in altloc 'B'. Problem is,<br>
altloc A and altloc B are different residue types, so phenix.refine<br>
exits stating that there are no common atoms when I enter the<br>
following NCS-type restraint:<br></blockquote><div><br></div><div>Wild guess - do you have a non-palindromic DNA helix bound in two different directions?</div><div><br></div><div>You can use the custom bond definitions to do this, but it's going to be messy. The documentation is here:</div>
<div><br></div><div><a href="http://www.phenix-online.org/documentation/refinement.htm#anch80">http://www.phenix-online.org/documentation/refinement.htm#anch80</a></div><div><br></div><div>You would need separate entries for each pair of atoms. I guess you'll want a distance_ideal of zero, and a small sigma (and perhaps slack). In the GUI, open Settings->Geometry restraints->Edit geometry restraints to add bonds. Might be easier to just write them out in a file and add that to the inputs list, however.</div>
<div><br></div><div>-Nat</div></div>