[phenixbb] DNA base pairing restraints work for GC only

Phoebe Rice price at uchicago.edu
Thu Oct 7 13:11:22 PDT 2010


We're trying to refine a large, low-resolution protein-DNA complex structure (4A in the good direction), and we need every restraint we can get, so I'm trying to use secondary structure restraints (in addition to ncs and 3 known substructure models).  

I found this from the newsletter: 
phenix.secondary_structure_restraints model.pdb > ss.eff
ran it, editted it, and plugged into the gui, where it seems to be taken into account if I also say "yes" to "find automattically".

Then I ran torsion angle dynamics to see if things were restrained as requested.  It only seems to be restraining G:C pairs - the ATs fly apart!
The log file makes a very suspicious set of remarks under "secondary structure":
No entry for base pair AT with type WWT (H=False).
 (repeated about the same # of times as we have AT pairs).

I thought maybe it was a nomenclature problem, but if "Gd" is OK I don't see what's wrong with "Ad", and the usual suspect, the thymine methyl, stays coplanar with the rest of its base, so the program must be recognizing our base/atom names.

Question 2 is that I wanted to view the restraints in pymol, but this command, also cribbed from the newsletter:
phenix.secondary_structure_restraints partry1noss.pdb ss_manual.eff format=pymol > h_bonds.pml
seems to overwrite the manual editing in my .eff file.

Help?  I'm new to phenix, so please be explicit about where I've gone wrong.

thanks, Phoebe

=====================================
Phoebe A. Rice
Dept. of Biochemistry & Molecular Biology
The University of Chicago
phone 773 834 1723
http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123
http://www.rsc.org/shop/books/2008/9780854042722.asp



More information about the phenixbb mailing list