On Thu, Oct 7, 2010 at 1:11 PM, Phoebe Rice
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".
A clarification: phenix.refine actually runs phenix.secondary_structure_restraints internally, and will run the automatic annotation if no helices/sheets/base pairs are found in the input parameters. So when refinement.secondary_structure.input.find_automatically=True, this is equivalent to running phenix.secondary_structure_restraints from scratch to generate new annotations. What happens when you leave that parameter set to the default? It should still use what was in the parameter file - otherwise, you may have found a bug.
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.
I think we were confused by the different conventions for DNA and RNA residue names in PDB files. Another user came across the same problem earlier this week, and it should be fixed in the latest nightly build (https://www.phenix-online.org/download/nightly_builds.cgi). If not, I can take a look if you send me the input model and parameters.
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.
I think the different parameter "scopes" are being confused (my fault). The parameter file should start and end like this: refinement.secondary_structure { . . . } If you make a copy and delete or comment out (insert #) the first and last lines, I think it will now be processed correctly. (You still want the original file for phenix.refine.) -Nat