On Fri, May 14, 2010 at 2:41 PM, Rajagopalan, Senapathy <span dir="ltr">&lt;<a href="mailto:SRajagopalan@tmhs.org">SRajagopalan@tmhs.org</a>&gt;</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;">




<div><font face="Calibri, Verdana, Helvetica, Arial"><span style="font-size:11pt">I am solving a protein-dna complex and Autobuild is able to build both the protein as well as DNA chain (one at a time). However, when I try to do the refinement, I get an error saying “Phenix could not find the geometry restraints in the standard monomer library for one or more residues in the pdb file... DG: 6 copies, DA: 3 copies, DT: 43 copies”. It seems like Autobuid uses the nomenclature DA, DC, DG and DT for the DNA bases while Phenix.Refine either doesn’t like the nomenclature or the restraint files uses a different one. It still however lets me do the refinement...although I don’t know if it just ignores the DNA part. Can someone enlighten me on this.<br>
</span></font></div></blockquote><div><br></div><div>This is just the GUI giving you the error, right?  I think this is just a stupid case-sensitivity error I made - should be an easy fix.  Could you please send me (not the list!) a relevant part of the PDB file (doesn&#39;t need to be the entire thing, just enough to give this error) so I can debug the problem?</div>
<div><br></div><div>If phenix.refine itself has any problem finding the appropriate restraints, it will quit with an error almost immediately after you start it - if this doesn&#39;t happen, you should be okay.</div><div>
<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div><font face="Calibri, Verdana, Helvetica, Arial"><span style="font-size:11pt">
Also, the nomenclature Coot seems to like is Ad, Cd, Gd, Td for the DNA and doesn’t like the above phenix style. In order to manipulate in coot, I had to rename all the bases...is it possible to have a format that is compatible both in Phenix and Coot or am I missing something obvious here.</span></font></div>
</blockquote><div><br></div><div>I really hope this isn&#39;t necessary - we should be using a similar monomer library.  What happens when you try to refine the file that was okay in Coot?  Could you send me that too (or an appropriate excerpt)?</div>
<div><br></div><div>thanks,</div><div>Nat</div></div>