I am glad to announce that the paper, titled "DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL", has recently been published in _Nucleic Acids Research_ (https://doi.org/10.1093/nar/gkz1222).
The DSSR program creates schematic block representations in diverse styles that can be seamlessly integrated into PyMOL and complement its other popular visualization options. In addition to portraying individual base blocks, DSSR can draw Watson-Crick pairs as long blocks and highlight the minor-groove edges. Notably, DSSR can dramatically simplify the depiction of G-quadruplexes by automatically detecting G-tetrads and treating them as large square blocks. The DSSR-enabled innovative schematics with PyMOL are aesthetically pleasing and highly informative: the base identity, pairing geometry, stacking interactions, double-helical stems, and G-quadruplexes are immediately obvious. These features can be accessed via four interfaces: the command-line interface, the DSSR plugin for PyMOL (written by Thomas Holder; http://pymolwiki.org/index.php/dssr_block), the web application (http://skmatic.x3dna.org/), and the web application programming interface. The web application interface (http://skmatic.x3dna.org/) also provides pre-calculated schematics and meta information of nucleic-acid-containing structures in the PDB. Here are some examples: * http://skmatic.x3dna.org/pdb/2lx1 * http://skmatic.x3dna.org/pdb/2grb * http://skmatic.x3dna.org/pdb/6vu1 * http://skmatic.x3dna.org/pdb_entries # 12 random entries * http://skmatic.x3dna.org/pdb_entries/recent-week * http://skmatic.x3dna.org/pdb_entries/recent-month The supplemental PDF (http://skmatic.x3dna.org/gkaa426-supp.pdf) has been written to serve as a practical guide, with complete and reproducible examples. Best regards, Xiang-Jun -- Xiang-Jun Lu (Ph.D.) Email: xiang...@x3dna.org Web: http://x3dna.org/ Forum: http://forum.x3dna.org/
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