> > I thought that some of the list members may be interested in the paper, > titled "DSSR-enabled innovative schematics of 3D nucleic acid structures > with PyMOL", recently published in _Nucleic Acids Research_ ( > https://doi.org/10.1093/nar/gkz1222).
*Sorry* about the wrong link to nar/gkz1222 -- I was reading that interesting paper on the U•A-U-rich RNA triple helix. The correct URL to the DSSR-PyMOL NAR paper is: https://doi.org/10.1093/nar/gkaa426 Best regards, Xiang-Jun -- Xiang-Jun Lu (Ph.D.) Email: xiang...@x3dna.org Web: http://x3dna.org/ Forum: http://forum.x3dna.org/ On Sat, May 23, 2020 at 1:41 PM Xiang-Jun Lu <3dna...@gmail.com> wrote: > 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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