Add RNA feature identification using DSSR

[3dna.lu@…]

The DSSR software identifies many basic features of RNA structures. We met with the author Xiang-Jun Lu in 2014 to discuss adding it to Chimera. It could be added to ChimeraX as a web service, or DSSR libraries could be included as a ToolShed tool.

The Chimera ticket about this is

​http://plato.cgl.ucsf.edu/trac/chimera/ticket/12866

Begin forwarded message:

From: Xiang-Jun Lu
Subject: Re: [Chimera] #12866: RNA secondary structure annotations
Date: May 10, 2017 at 11:24:38 AM PDT
To: "chimera-bugs@…" <chimera-bugs@…>, Tom Goddard
Cc: Nikolai Ulianov

Dear Tom,

We communicated three years ago on connecting DSSR with Chimera. Over the years, I've continuously refined DSSR and expanded its features. The DSSR paper was published in 2015 in NAR: [DSSR: an integrated software tool for dissecting the spatial structure
of RNA](​https://doi.org/10.1093/nar/gkv716). Significantly, a follow-up paper (see attached), titled [DSSR: an integrated software tool for dissecting the spatial structure of RNA](​https://doi.org/10.1093/nar/gkv716), has recently been published. Check the DSSR-Jmol website (​http://jmol.x3dna.org) for more info.

The [DSSR-Jmol integration](​http://jmol.x3dna.org) described therein bridges the DSSR 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. The DSSR-Jmol integration fills a gap in RNA structural bioinformatics, serving a huge user base of researchers, educators, and students alike.

If you're interested in bringing similar RNA features into Chimera, please let me know. I'd be happy to work with someone who has a *deep knowledge of Chimera* to better connecting DSSR with it.

By the way, Thomas Holder has written a DSSR-plugin for PyMOL (​https://pymolwiki.org/index.php/Dssr_block) that brings the schematics base (and Watson-Crick base-pair) rectangular blocks into PyMOL.

Best regards,

Xiang-Jun