[phenixbb] Secondary structure restraints for nucleic acids

Nathaniel Echols nechols at lbl.gov
Fri Apr 2 09:59:31 PDT 2010

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:


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.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20100402/a19c1224/attachment-0003.htm>

More information about the phenixbb mailing list