[phenixbb] nucleic acid secondary restraints breaking in 1.7.1-743

Francis E Reyes Francis.Reyes at Colorado.EDU
Tue Aug 16 09:48:39 PDT 2011

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  


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

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