Hi Lisa,
I am not an phenix expert and, as Ed mentioned, from the message that
refinement failed it is hard to figure out what or how it failed.
Nevertheless, here are a few suggestions.
-do your alternate conformations make consistent sets? E.g. do the AADE
and AGUA both belong to the linked set and the BADE and BGUA both belong
to the broken set?
-I would give the water a lower then 0.5 occupancy. For refmac it is
claimed that the steric repulsions are switched off between atoms if the
combined occupancies are less or equal to one.
-tackle one problem at a time, i.e. remove the water first and see that
the conneced/broken strands are being refined correctly. Once that is
ok, you could add the water.
my two cents,
Herman
________________________________
From: CCP4 bulletin board [mailto:[email protected]] On
Behalf Of LISA
Sent: Friday, May 25, 2012 1:02 PM
To: [email protected]
Subject: [ccp4bb] alternative conformation refinement by phenix
Hi all,
I am refining a DNA-protein complex structure by phenix. My
protein is a nuclease and the DNA bound to protein is a mixture of the
substrate and product. Partial DNA was cleavaged by the protein and
others is keep a un-cleavaged strand. I am trying to rerine this mixture
with phenix. My DNA sequence is NNNNAGNNNNNN. Half of DNA was cleavaged
between AG and half DNA keep a uncleavaged strand as my sequence.
Nucleic acid AG have two conformations in this structure and a water
molecule located close to the phosphate group when it uncleavaged. I
defined AADE and BADE, AGUA and BGUA with 0.5 occupancy. I also give the
water mentioned above 0.5 occupancy. I try to refine this structure by
phenix but failed. Please give me some suggestion about this DNA
alternative confromation refinement? How should I define the occ.params
file? Thank you in advance.
Lisa
