Hot off the presses...
https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkx365
*DSSR-enhanced visualization of nucleic acid structures in Jmol*
*Abstract*
Sophisticated and interactive visualizations are essential for making sense
of the intricate 3D structures of macromolecules. For proteins, secondary
structural components are routinely featured in molecular graphics
visualizations. However, the field of RNA structural bioinformatics is
still lagging behind; for example, current molecular graphics tools lack
built-in support even for base pairs, double helices, or hairpin loops.
DSSR (Dissecting the Spatial Structure of RNA) is an integrated and
automated command-line tool for the analysis and annotation of RNA tertiary
structures. It calculates a comprehensive and unique set of features for
characterizing RNA, as well as DNA structures. Jmol is a widely used,
open-source Java viewer for 3D structures, with a powerful scripting
language. JSmol, its reincarnation based on native JavaScript, has a
predominant position in the post Java-applet era for web-based
visualization of molecular structures. The DSSR-Jmol integration presented
here makes salient features of DSSR readily accessible, either via the
Java-based Jmol application itself, or its HTML5-based equivalent, JSmol.
The DSSR web service accepts 3D coordinate files (in mmCIF or PDB format)
initiated from a Jmol or JSmol session and returns DSSR-derived structural
features in JSON format. This seamless combination of DSSR and Jmol/JSmol
brings the molecular graphics of 3D RNA structures to a similar level as
that for proteins, and enables a much deeper analysis of structural
characteristics. It fills a gap in RNA structural bioinformatics, and is
freely accessible (via the Jmol application or the JSmol-based website
http://jmol.x3dna.org).
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
