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_Alpha... http://www.rsc.org/shop/books/2008/9780854042722.asp