<div dir="ltr"><div class="gmail_extra">On Tue, Nov 5, 2013 at 7:46 AM, Ryan Spencer <span dir="ltr"><<a href="mailto:rspencer@uci.edu" target="_blank">rspencer@uci.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"><div lang="EN-US" link="blue" vlink="purple"><p class="MsoNormal"><span style="color:rgb(31,73,125);font-family:Calibri,sans-serif;font-size:11pt"> The pdb of the ligand probably had an occupancy of 0.00 when you brought it into Coot. The easiest way to handle it is to just change all the occupancies of the ligand back to 1.00 in the pdb. If the ligand has partial occupancy then phenix might be dropping it down to 0.00 if you have the ‘refine occupancies’ box checked. I’ve seen this before when doing MR with ligands that phenix does not recognize without the corresponding .cif.</span></p>
</div></blockquote><div><br></div><div style>That actually has nothing to do with the CIF - by default Phaser will set the occupancy to zero for anything labeled as a heteroatom (i.e. HETATM lines in a PDB file), which the exception of some non-standard or modified amino acids such as MSE. It's not clear if that's what's happening in Wei's case; I'm pretty sure eLBOW doesn't normally output ligands with an occupancy of zero.</div>
<div style><br></div><div style>-Nat</div></div></div></div>