Some list members may be interested in a paper, titled ["DSSR-enhanced
visualization of nucleic acid structures in Jmol"](
https://doi.org/10.1093/nar/gkx365), recently published in *Nucleic Acids
Research* (NAR). The [DSSR-Jmol integration](http://jmol.x3dna.org)
described therein bridges the DSSR (Dissecting the Spatial Structure of
RNA) command-line analyzing tool and the Jmol molecular viewer seamlessly
together via a simple JSON interface. Now users can select DSSR-derived RNA
structural features (such as base pairs, double helices, various loops,
etc.) and visualize them in several new representations in Jmol
*interactively*. Moreover, fine-grained characteristics of these features
can be queried via the Jmol SQL for DSSR. Here are some examples:
# Jmol 14.13.1 (2017-04-09) or later
load =1ehz/dssr # load yeast phenylalanine tRNA to Jmol with DSSR
annotation
cartoon only; set cartoonSteps
rotate best; rotate z 90
color PROPERTY DSSR stems
# Jmol selections enabled by the DSSR-Jmol integration
SELECT hairpins # select the three hairpin loops
SELECT junctions # select the four-way junction loop
select within(dssr, "nts WHERE is_modified") # select modified
nucleotides (14 in total)
SELECT within(dssr, "pairs WHERE name != 'WC'") # select
non-Watson-Crick pairs
SELECT within(dssr, "pairs WHERE name = 'WC' OR name = 'Wobble'") #
select canonical pairs
Select within(dssr, "pairs WHERE name != 'WC' AND name != 'Wobble'") #
select non-canonical pairs
SELECT within(dssr, "pairs WHERE LW = 'tSW'") # select pairs of type
'tSW', per Leontis-Westhof
The DSSR-Jmol integration fills a gap in RNA structural bioinformatics,
serving a huge user base of researchers, educators, and students alike.
Give http://jmol.x3dna.org a try, and you may find it useful for exploring
RNA/DNA structures.
A summary of key links:
* [DSSR-Jmol website](http://jmol.x3dna.org)
* [DSSR-Jmol NAR paper (open access)](https://doi.org/10.1093/nar/gkx365)
* [Details for reproducing reported results](
http://forum.x3dna.org/dssr-jmol-integration/)
* [DSSR-Jmol manual](http://jmol.x3dna.org/dssr-jmol-manual.pdf)
Best regards,
Xiang-Jun
[This message is posted on ccp4bb and pdb-l. Sorry for an extra copy of it
you may receive.]
--
Xiang-Jun Lu (PhD)
Email: xiang...@x3dna.org
Web: http://x3dna.org/
Forum: http://forum.x3dna.org/
