Thanks Nat I've used this before and is useful when you have an already built structure (either your target structure or some simple A-form helices). For simple helices, it would be easier to specify a textual string and have phenix generate the proper restraints for phenix.refine (dihedrals, h-bonds, angles, etc). An excellent textual format for doing this is via stockholm. ftp://selab.janelia.org/pub/software/infernal/Userguide.pdf , specifically the SS_cons line.. (See the tRNA example in there). The current workflow, is to use coot to build an A-form helix and upload the file to PDBrestraints or use phenix.secondary_structure_restraints. Either case requires a sample pdb. F On Aug 15, 2011, at 9:51 AM, Nathaniel Echols wrote:
This may be a good intermediate solution:
http://rna.ucsc.edu/pdbrestraints/
I had meant to add an option to output the base pair restraints using the existing custom bond syntax, but haven't had time to do that yet.
-Nat
--------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder