[phenixbb] Secondary structure restraints for nucleic acids

Peter Grey petgxray at gmail.com
Fri Apr 2 11:45:59 PDT 2010

So in the mean time until this is implemented in Phenix I recommend the
following Web-server, by Martin Laurberg, that generates custom RNA/DNA
base pairing restraints and produces appropriate files for Phenix :



On Fri, Apr 2, 2010 at 6:59 PM, Nathaniel Echols <nechols at lbl.gov> wrote:

> On Thu, Apr 1, 2010 at 4:12 AM, Peter Grey <petgxray at gmail.com> wrote:
>> Dear developers,
>> Does the new mechanism of secondary structure restraints apply to nucleic
>> acids as well  ?  Are the average bond distances similar and does DSSP works
>> well with RNA/DNA ?
> No.  The DSSP algorithm only deals with proteins, and the hydrogen bonding
> patterns in proteins are much easier to describe using reduced
> representations (3 types of helix, 2 types of sheet) than for nucleic acids.
>  As always, you can specify hydrogen bonds individually using the custom
> bond definitions in phenix.refine:
> http://www.phenix-online.org/documentation/refinement.htm#anch80
> Jeff Headd started working on extracting H-bond information from the output
> of Probe, but I think we were still trying to figure out a more elegant way
> of storing these.  Specifying helices with Watson-Crick bonding alone is
> going to miss many of the interactions in large RNAs, so listing individual
> bonds may be the best option.  It would probably not be difficult to add a
> command to generate the list automatically (e.g.
> "phenix.base_pair_restraints").  We are working on ways to make these bonds
> easier to manage and visualize, and Bradley Hintze (Richardson lab, formerly
> Sean Johnson's lab) has written a PyMOL plugin to pick and display
> individual bonds and generate phenix.refine restraints (which I can't find
> online, but I can email him if you're interested).
> I have no idea what the appropriate distances are in nucleic acids - I
> imagine they're similar for genuine H-bonds (~1.975A), but probably more
> varied if you try to approximate them without hydrogens.
> -Nat
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