DNA Homepage Nucleic Acid Structures.The DSSR Jmol paper, titled DSSR enhanced visualization of nucleic acid structures in Jmol, has been officially published in the 2.Nucleic Acids Research NAR.Notably, the work has been featured in the cover image, as shown below Caption 3.D interactive visualization of selected RNA structural features enabled by the DSSR Jmol integration http jmol.Clockwise from upper left Structure of the xpt pbu.X guanine riboswitch in complex with hypoxanthine PDB id 4fe.The three way junction loop encompassing the metabolite in space filling representation is color coded by base identity A, red C, yellow G, green U, cyan.The loop loop interaction a kissing loop motif at the top is highlighted in red upper left corner.Structure of the Thermus thermophilus 3.S ribosomal subunit in complex with antibiotics PDB id 1fjg in step diagram.Atlas Translation Software Website' title='Atlas Translation Software Website' />West Coast Internet, an Internet Service Provider ISP.The 1. Cinema 4D Software Free Download Crack Autocad here. S ribosomal RNA is color coded in spectrum with the 5 end in blue and the 3 end in red upper middle.Structure of the classic L shaped yeast phenylalanine t.RNA PDB id 1ehz in step diagram, with the three hairpin loops highlighted in red and the 2,1,5,0 four way junction loop in blue upper right corner.Structure of the Pistol self cleaving ribozyme PDB id 5ktj, showcasing in red the horizontal helix in space filling representation.The helix is composed of six short stems stabilized via coaxial stacking interactions bottom.The DSSR Jmol integration bridges the DSSR command line analyzing tool and the Jmol molecular viewer seamlessly together via the standard JSON interface.Now users can select DSSR derived RNA structural features such as base pairs, double helices, various loops, etc.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, and brings RNA visualization to an entirely new level.Atlas Translation Software Website' title='Atlas Translation Software Website' />The web interface http jmol.Featured as the cover image of the 2.NAR web server issue, DSSRs publicity would surely increase through the DSSR Jmol integration.Additionally, Ive written a new post on the 3.DNA Forum that provides the scripts and datafiles used to create the cover image.I am pleased to announce the advance online, May 3, 2.DSSR enhanced visualization of nucleic acid structures in Jmol in Nucleic Acids Research NAR.Co authored by Robert Hanson Jmol and me DSSR, the article will appear in the July 2.NAR.Here are the key links related to the paper The DSSR Jmol integration project was initiated in October 2.I approached Bob at a meeting organized by RCSBPDB at Rutgers.Thereafter, we met only once in July 2.Paris.Over the years, we have mostly communicated via email, occasionally facilitated by Skype.Atlas Translation Software Website' title='Atlas Translation Software Website' />Our work bridges the DSSR command line analyzing tool and the Jmol molecular viewer together via a simple JSON interface and a powerful query language.Users can now select DSSR derived RNA structural features such as base pairs, double helices, and various loops as easily as they can select protein alpha helices and beta strands.Moreover, fine grained characteristics of these features can be queried via Jmol SQL for DSSR see examples below.Notably, the novel representation styles step diagram and base blocks and coloring schemes bring RNA visualization to an entirely new level see Figure 3 of the paper.RNA to Jmol with DSSR annotation.SELECT hairpins select the three hairpin loops.SELECT junctions select the four way junction loop.WHERE ismodified select modified nucleotides 1.SELECT withindssr, pairs WHERE name WC select non Watson Crick pairs.SELECT withindssr, pairs WHERE name WC OR name Wobble select canonical pairs.Select withindssr, pairs WHERE name WC AND name Wobble select non canonical pairs.SELECT withindssr, pairs WHERE LW t.SW select pairs of type t.SW 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.Its functionality is freely accessible either via the Jmol application, or the JSmol based website http jmol.By adhering to web standards, the website is fully functional in all modern browsers on various computeroperating systems including handheld devices, such as tablets and smart phones.The web interface is simple and intuitive, and new users can get started easily.It also allows power users to take full advantage of Jmol scripting via a command line console.This work also provides an example for integrating DSSR derived features into other molecular graphics programs or bioinformatics pipelines involving nucleic acid structures.By design, DSSR is a stand alone, command line program written in ANSI C.The binary executables are only 1.MB in size, and self contained.With zero dependencies, no setup or configuration, it is trivial to get DSSR up and running.DSSR uncovers a wide range of RNADNA structural features in a consistent, easily accessible framework.Wordle is a toy for generating word clouds from text that you provide.The clouds give greater prominence to words that appear more frequently in the source.Topics Replies Views Last post DKC2 Unveiled Short link Started by emptysys Yesterday, 1025 pm 1 Replies.Delphic Oracle and Timaeus astrological software.Information on Hellenistic, Medieval and Vedic natal astrology.It possesses a much richer set of functionalities for nucleic acid structural analysis see the DSSR User Manual than any other existing tools I am aware of.Pc Games Demos Blogspot Grand Theft Auto Gta Download Games '>Pc Games Demos Blogspot Grand Theft Auto Gta Download Games .Moreover, the program is efficient and robust, making it an ideal component to be integrated into other pipelines, especially via the standard and structured JSON interface.Collaborating with Bob has been a truly exciting experience.The NAR web publication represents a gratifying intermediate result along an on going journey.Hopefully, others may be some of you can join us in pushing forward the field of RNA structural bioinformatics.Recently, while analyzing a representative set of RNA structures from the PDB, I came across three weird entries.They are documented below, primarily for my own record.Structure of the KH domain of T STAR in complex with AAAUAARNA.There are two alternative conformations for the six nt AAAUAARNA component, labeled A and B, respectively.Normally, the AB alternative coordinates for each atom are put directly next to each other, and assigned the same chain id, as in 1msy for the phosphate group of G2.A.In 5els, however, the two alternative conformations AB are separated into two chains chain H for A, and chain I for B.The structure of the transition state analogue DCSN bound to the large ribosomal subunit of Haloarcula marismortui.The three nt fragment DA1.C1.C1. 81 on chain 4 is in the 3 5 direction.The crystal structure of m6A RNA with the YTHDC1 YTH domain.The mm.CIF file has a model number of 0, instead of 1 as in other cases I am aware of.Dear 3.DNA Forum subscribers,Note If youve difficulty in accessing the 3.DNA homepage, possibly the case from mainland China as I know it, please visit its duplicate at http home.This newsletter is written in Markdown, with a translated HTML version posted on the 3.DNA homepage.DNA v.The C source code is now available.Since the programs are written in strict ANSI C, 3.DNA can be compiled as is on any computersoperating systems with a C or C compiler.For user convenience, three binary distributions with source code under the src subdirectory are provided for Windows, Linux, and Mac OS X.The distributed Windows version works in native Windows 7 and up, via the cmd command line interface, or Con.EMU, Min.GWMsys Msys.Cygwin, in either 3.A new set of simple base pair and step parameters was introduced to give intuitive numerical values for non Watson Crick base pairs and associated steps.See the short communication titled Characterization of base pair geometry in the January 2.Computational Crystallography Newsletter CCN.The fiber program includes a new option, pauling, for easy generation of Pauling Corey triplex models of DNARNA with arbitrary base sequence.See my blogpost titled Paulings triplex model of nucleic acids is available in 3.DNA.Thomas Holder Py.MOL Principal Developer at Schrdinger, Inc.Py.
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