[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

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