[phenixbb] unwanted disulfids and geometry restraints

Ursula Schulze-Gahmen uschulze-gahmen at lbl.gov
Wed Jun 26 15:40:32 PDT 2013

I have 2 questions:

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

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?


Ursula Schulze-Gahmen, Ph.D.
Assistant Researcher
UC Berkeley, QB3
356 Stanley Hall #3220
Berkeley, CA 94720-3220
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20130626/b4fd5c07/attachment.htm>

More information about the phenixbb mailing list