The DSSR-Jmol and DSSR-PyMOL integrations

As documented in the Overview PDF, DSSR can be easily incorporated into other structural bioinformatics pipelines. Working with Robert Hanson and Thomas Holder respectively, I initiated the integrations of DSSR into Jmol and PyMOL, two of the most popular molecular viewers. The DSSR-Jmol and DSSR-PyMOL integrations lead to unparalleled search capabilities and innovative visualization styles of 3D nucleic acid structures. They also exemplify the critical roles that a domain-specific analysis engine may play in general-purpose molecular visualization tools.

On January 27, 2016, I wrote the blogpost Integrating DSSR into Jmol and PyMOL. Four years later, these integrations have led to two peer-reviewed articles, both published in Nucleic Acids Research (NAR). This blogpost (dated 2020-09-15) highlights key features in each case and reflects on my experience in these two exciting collaborations.

The DSSR-Jmol integration

Hanson RM and Lu XJ (2017). DSSR-enhanced visualization of nucleic acid structures in Jmol. The DSSR-Jmol integration excels in its SQL-like, flexible searching capability of structural features, as demonstrated at the website http://jmol.x3dna.org. This work fills a gap in RNA structural bioinformatics by enabling deep analyses and SQL-like queries of RNA structural characteristics, interactively. Here are some simple examples:

SELECT WITHIN(dssr, "nts WHERE is_modified = true") # modified nucleotides
SELECT pairs # all pairs
Select WITHIN(dssr, "pairs WHERE name = 'Hoogsteen'") # Hoogsteen pairs
SELECT WITHIN(dssr, "pairs WHERE name != 'WC'") # non-Watson-Crick pairs
SELECT junctions # all junctions loops
select within(dssr, "junctions WHERE num_stems = 4") # four-way junction loops

In a recently email communication, Bob wrote:

How are you doing? I’m smiling, because I am remembering our incredible, animated discussions and how fun it was to work together with you on Jmol and DSSR.

The DSSR-PyMOL integration

Lu XJ (2020). DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL. The DSSR-PyMOL integration brings unprecedented visual clarity to 3D nucleic acid structures, especially for G-quadruplexes. The four interfaces cover virtually all conceivable use cases. The easiest way to get started and quickly benefit from this work is via the web application at http://skmatic.x3dna.org.

I approached Thomas to write the DSSR-PyMOL manuscript together, in a similar way as the DSSR-Jmol paper. He wrote back, saying “I’m not interesting in being co-author of the paper”, adding:

But, if there is anything I can help you with, like revising the `dssr_block.py` script, or proof-reading the PyMOL related parts of the manuscript, I’ll be happy to do so.

Indeed, Thomas helped in several aspects of the DSSR-PyMOL project, as acknowledged in the paper:

I appreciate Thomas Holder (PyMOL Principal Developer, Schrödinger, Inc.) for writing the DSSR plugin for PyMOL, and for providing insightful comments on the manuscript and the web application interface.

Enhanced vs Innovative

Some viewers may noticed the difference in titles of the two NAR papers: “DSSR-enhanced visualization of nucleic acid structures in Jmol” vs. “DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL”. As a matter of fact, the initial title of the DSSR-PyMOL paper was DSSR-enhanced visualization of nucleic acid structures in PyMOL, as shown in the December 02, 2019 announcement post on the 3DNA Forum.

In an era where reproducibility of “scientific” publications has become an issue and “break-throughs” are often broken or hardly held, I hesitate to use phrases such as “innovative”, “novel”, “paradigm shift” etc. Instead, I often use the modest words “refinement”, “enhance”, “improved”, “revised” etc, and try to deliver more than claimed. However, reviewers may take solid work but modest writing as “incremental” or “unexciting”. Before submitting the DSSR-PyMOL paper, I changed the title to DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL. Does it mean that the DSSR-PyMOL integration is more innovative than the DSSR-Jmol case? Not necessarily. I do have a paper with “innovative” in its title.

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