<div dir="ltr">Hi, I'm trying to use phenix.ensemble_refinement, and my structure has several zinc atoms, both coordinated to amino acids and free imidazoles, and sometimes both. It looks as though it's not really understanding that the zincs really should stay more or less in their coordination spots, and are spending some time in kind of weird spots. I couldn't find anything documented that seems like it will help, unless there's some clever way to use the harmonic restraints for this that I haven't figured out.<div>
<br></div><div>And while I'm at it, I have another potentially related problem: the rfree of my final ensemble (0.27) is substantially higher than my input structure (0.24). And yes, I had been doing my refinement in phenix, with hydrogens added, and I optimized pTLS. If you're curious, this is a 1.9 A structure.<br>
<div><br></div><div>Any help and/or suggestions would be greatly appreciated!<br><div><div><br></div><div>Thanks,</div><div>Scott</div><div><br></div>-- <br><div dir="ltr"><div style="font-family:Helvetica;word-wrap:break-word">
<font>Scott Horowitz, Ph.D.<br></font></div><div style="font-family:Helvetica;word-wrap:break-word"><font>Research Associate</font></div><div style="font-family:Helvetica;word-wrap:break-word"><font>Howard Hughes Medical Institute</font></div>
<div style="font-family:Helvetica;word-wrap:break-word"><font><br>University of Michigan<br>Department of Molecular, Cellular, and�Developmental Biology<br>Bardwell lab<br>830 N. University Ave, Room 4007<br>Ann Arbor, MI 48109<br>
phone:�<a value="+17346476683" style="color:rgb(17,85,204)">734-647-6683</a><br>fax:�<a value="+17346154226" style="color:rgb(17,85,204)">734-615-4226</a></font></div></div>
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