I have 2 questions:<br><br>1)  I am using phenix.refine on the command line with a .eff file as input that was modified from previous GUI phenix runs. My structure has several Zn atoms and readyset creates a geometry_restraints file for the Zn interactions. I am not sure if phenix.refine gets these restraints when I run it from the command line. Do I need to read this file in some specific way?<br>
<br>2) The other question is: phenix refines several of the Cysteine neighbors in the Zn environment as disulfids, but they are not. How do I prevent this from happening?<br><br>Ursula<br clear="all"><br>-- <br>Ursula Schulze-Gahmen, Ph.D.<br>
Assistant Researcher<br>UC Berkeley, QB3<br>356 Stanley Hall #3220<br>Berkeley, CA 94720-3220<br>