[PyMOL] Reproduce results in the DSSR paper

A paper titled "DSSR, an integrated software tool for dissecting the
spatial structure of RNA" recently appeared in *Nucleic Acids Research* (
http://nar.oxfordjournals.org/cgi/content/full/gkv716). Starting from a
three-dimensional atomic coordinate file in either PDB or PDBx/mmCIF
format, DSSR, the new software product described in the paper, analyzes and
annotates RNA tertiary structures and uncovers a broad range of structural
features in a consistent and easily accessible framework. The software is
implemented in ANSI C as a stand-alone, command-line program and is
self-contained. The binaries for common operating systems (Mac OS X, Linux,
and Windows) are tiny (<1MB), without runtime dependencies on third-party
libraries. DSSR is efficient and robust due to comprehensive tests against
all nucleic-acid-containing structures in the PDB and continued refinements
based on user feedback.

DSSR identifies canonical and noncanonical base pairs, including those with
modified nucleotides, in any tautomeric or protonation state. The software
detects higher-order (three or more) coplanar base associations, termed
multiplets. It finds arrays of stacked pairs, classifies them by base-pair
identity and backbone connectivity, and distinguishes a stem of covalently
connected canonical pairs from a helix of stacked pairs of arbitrary
type/linkage. DSSR also pinpoints the coaxial stacking of multiple stems
within a single helix and lists the isolated canonical pairs that lie
outside of a stem. The program characterizes "closed" loops of various
types (hairpin, bulge, internal, and junction loops) and pseudoknots of
high complexity. Notably, DSSR employs isolated pairs and the ends of
stems, whether pseudoknotted or not, to define junction loops. This new,
inclusive definition provides a novel perspective on the spatial
organization of RNA, even for small molecules such as the viral tRNA mimic
from turnip yellow mosaic virus and the *env22* twister ribozyme.

In short, DSSR is to RNA what DSSP is to proteins for defining secondary
structures, but with more functionality: DSSR includes quantitative
descriptions of local base-pair geometry; assignments of common names and
classifications of base pairs; listings of commonly used sugar-phosphate
backbone parameters, continuous base stacks, and non-pairing interactions
(including those involving phosphate groups); and detections of ribose
zipper motifs, A-minor motifs, G-tetrads, U-turns, kissing loops, and
kink-turns.

The publication includes significant new scientific findings that are
enabled by the innovative analysis algorithms implemented in the software.
Moreover, the paper introduces an appealing and highly informative
"cartoon-block" representation of RNA structure that combines PyMOL cartoon
schematics with color-coded rectangular base (or base-pair) blocks. As a
follow-up to the publication, the 3DNA Forum includes all of the scripts
and data files associated with the article in a new section titled
"DSSR-NAR paper" (http://forum.x3dna.org/dssr-nar-paper/). The Forum also
contains links to an updated version of the DSSR User Manual (
http://x3dna.bio.columbia.edu/docs/dssr-manual.pdf). Any interested party
should be able to reproduce the tabulated data and figures (including the
supplementary data) reported in the article. Moreover, with the details
provided in "RNA cartoon-block representations with PyMOL and DSSR" (
http://forum.x3dna.org/dssr-nar-paper/rna-cartoon-block-representations-with-pymol-and-dssr/),
schematic images identical to those in the paper and the post can be easily
generated. Any questions related to the paper are welcomed on the 3DNA
Forum. Dr. Xiang-Jun Lu, the lead author of the paper and the person
spearheading the Forum, aims to respond promptly to any reported issues.

[This message is cross-posted on ccp4bb, pdb-l, and pymol-users. I
apologize for any duplicate copies you may receive.]

Xiang-Jun

--
Xiang-Jun Lu (PhD)
Email: xia...@x3...
Web: http://x3dna.org/
Forum: http://forum.x3dna.org/