3DNA is a versatile, integrated software system for the analysis, rebuilding, and visualization of three-dimensional nucleic-acid-containing structures. The software is applicable not only to DNA (as the name 3DNA may imply) but also to complicated RNA structures and DNA-protein complexes. In 3DNA, structural analysis and model rebuilding are two sides of the same coin: the description of the structure is rigorous and reversible, thus allowing for its exact reconstruction based on the derived parameters. 3DNA automatically detects all non-canonical base pairs, base triplets and higher-order associations (collectively termed multiplets), and coaxially stacked helices; provides a comprehensive collection of fiber models of regular DNA and RNA helices; generates highly effective schematic presentations that reveal key features of nucleic-acid structures; performs undisturbed, and have facilities for the analysis of molecular dynamics simulation trajectories. It is a representative of what would become the brand new version 3 of 3DNA.
DSSR consolidates, refines, and significantly extends the functionality of 3DNA v2.x for RNA structural analysis. 3DNA contains 55 fiber models compiled from literature, plus a derived RNA model (as of v2.1). To the best of my knowledge, this is the most comprehensive collection of regular DNA/RNA models.
Please see for detailed structural features of these models and references. The 55 models are based on the following works:. Chandrasekaran & Arnott (from #1 to #43) — the most well-known set of fiber models.
Alexeev et al. (#44-#45). van Dam & Levitt (#46-#47). Premilat & Albiser (#48-#55) The utility program fiber makes the generation of all these fiber models in a simple, consistent interface, and produces coordinate files in either PDB or PDBML format. Of those models, some can be built with an arbitrary sequence of A, C, G and T (e.g., A-/B-/C- DNA from calf thymus), while others are of fixed sequences (e.g., Z- DNA with GC repeats). The sequence can be specified either from command-line or a plain text file, in either lower, UPPER, or MixED cases. Once 3DNA in properly installed, the command-line interface is the most versatile and convenient way to generate, e.g., a regular double-stranded DNA (mostly, B- DNA) of arbitrary sequence.
As of release v2.3-2016sept06, the C source code of the 3DNA software package is available. The code can be found in the $X3DNA/src folder of the distributed tarballs for Linux, Mac OS X, and Windows. Since 3DNA is written in pure ANSI C, it can be compiled without changes on any platform with a modern C compiler. The original codebase of 3DNA was written around year 2000. Up until v2.3, the infrastructure of 3DNA has remained stable for 16 years. During the time, 3DNA has been widely adopted in other bioinformatics pipelines and cited over 1,500 times. Over the years, I’ve received quite a few requests for 3DNA source code.
However, due to complications of various factors (including software licensing), 3DNA had only been distributed in executable forms for the crucial C programs. Now, the C code of 3DNA is finally open source!
As before, users need to register on the to download the software. The download page also includes x3dna-v2.0.tar.gz that accompanied the 2008, and x3dna-v1.5.tar.gz that corresponded to the. Other than minor revisions to pass strict gcc compiler options, the v1.5 and v2.0 codebases are kept as they were. 3DNA is backward-compatible as far as the key base-pair parameters are concerned. Moreover, between v1.5 and v2.0, the command-line interface stays the same.
The two previous versions are released for historical reasons. For example, one may notice some obvious “similarities” between 3DNA v1.5 and RNAView. The development of DSSR and SNAP will push 3DNA into a brand new version (v3), which contains significant changes in functionality and interface, and is no longer compatible with previous versions. I intend to keep 3DNA v2.3 in a ‘maintenance’ mode: no new features are planed, but bug reports and user questions will be promptly addressed on the 3DNA Forum, as always. Making 3DNA open source should help further prompt its adoptions, and adaptations in structural bioinformatics of nucleic acids.
There are numerous types of software licenses, but none of them seems to be a good fit for my purpose. As a result, I’ve come up with a permissive “ citation-ware” license with contents as below: 3DNA is a suite of software programs for the analysis, rebuilding and visualization of 3-Dimensional Nucleic Acid structures. Permission to use, copy, modify, and distribute this suite for any purpose, with or without fee, is hereby granted, and subject to the following conditions: At least one of the 3DNA papers must be cited, including the following two primary ones: 1. J., & Olson, W. '3DNA: a software package for the analysis, rebuilding and visualization of three‐dimensional nucleic acid structures.'
Nucleic Acids Research, 31(17), 5108-5121. J., & Olson, W. '3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures.' Nature Protocols, 3(7), 1213-1227. THE 3DNA SOFTWARE IS PROVIDED 'AS IS', WITHOUT EXPRESSED OR IMPLIED WARRANTY OF ANY KIND.
Any 3DNA-related questions, comments, and suggestions are welcome and should be directed to the open 3DNA Forum (http://forum.x3dna.org/). Upon user requests, I’ve recently introduced the -block-color option to DSSR, available as of v1.5.2-2016apr02. As its name implies, the -block-color option facilitate user customization of PyMOL rendered colors of the base rectangular blocks or their edges (e.g., the minor-groove) directly from the command-line.
A simple example goes like this: -block-color='A blue; T red', which makes A colored blue and T colored red. As detailed below, the new option is very flexible with regard to the specification of colors, bases, or some edges to highlight. Before that, a little background is in order. Background info The DSSR cartoon-block representation follows the color convention of the original 3DNA blocview script, where A is red; C is yellow; G is green; T is blue; and U is cyan. If I remember correctly, the blocview coloring was based on the scheme adopted by the Nucleic Acid Database ( NDB). To allow for some flexibility, 3DNA includes a config file named $X3DNA/config/raster3d.par where users can change the values of the corresponding bases. However, I do not know if any user has ever bothered to play around with the configuration file for customized base colors.
Over the years, blocview-generated images have become popular, due to its simplicity, and (maybe more importantly) its endorsement by the NDB and PDB for nucleic acid structures. Via NDB, the blocview-generated images have also been used in and. Nevertheless, the blocview script has several dependencies: for protein or DNA/RNA backbone ribbons, render from for rendering, and for image processing.
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Moreover, the blocview script used by NDB/PDB is (likely to be) based on 3DNA v1.5, the last version before I left Rutgers in 2002. Over the years, 3DNA has been continuously refined, with significant changes introduced in v2.0 around 2008 to accompany the. Currently at v2.3, the codebase for 3DNA version 2 is in maintenance mode: the software will still be supported with identified bugs fixed, but no more new feature is planned. 3DNA version 3, as represented by DSSR and SNAP, is the way to go. DSSR has no third-party dependencies While creating DSSR, I set it as one of the design goals to make the program fully self-contained, without any third-party dependencies.
Connections to other tools are clearly delineated via text files. If anything goes wrong, one can easily identify where the problem is. Legend of korra season 2 torrent download. Experience over the past few years has unambiguously proved the effectiveness of this zero-dependency approach.
Other than being directly distributed with an operating system, DSSR is the easiest to get up and running. Moreover, DSSR can be easily integrated into other pipelines, including Jmol and PyMOL, among many other bioinformatics tools. For the cartoon-block representation, DSSR produces.r3d files that can be loaded into PyMOL, mixed and matched with other visualization styles PyMOL has to offer. No more direct dependencies on MolScript, Raster3D, and ImageMagick as is the case for blocview. It is also worth mentioning that DSSR does not need PyMOL to run. DSSR and PyMOL are connected via.r3d files, a process which can be streamlined with the PyMOL plugin. DSSR releases before v1.5.2-2016apr02 have the color coding of base blocks fixed within the source code, following the default style of blocview.
Over the past few months, I’ve received at least two explicit requests on customizing the default colors of DSSR-generated base blocks. The -block-color option has been introduced for this purpose. Details of the -block-color option The general format of the option is as follows: -block-color='id color ; id2 color2.' . id can be A, C, G, T, U, or the degenerated IUPAC code, including R, Y, N etc. See for details. id can also be minor, major, upper, bottom, wc-edge to specify one of the six faces of a 3D rectangular block.
See for details. id can further be GC, AT, GU, pair, and variants thereof, to specify the colors of the corresponding long base-pair rectangular blocks. color can be a common name (144 total), as specified in the website. For example, red, magenta, light gray etc. color can also be a single number in the range 0, 1 or 0, 255 to specify a shade of gray. DSSR repeat the number twice to get the RGB triple consisting of the same number.
color can further be a set of three space-delimited numbers to specify the RGB triple. Again, the number can be in 0, 1 or 0, 255. Moreover, the three numbers can be put in square brackets. For example -block-color='A 0 1 1' and -block-color='A 0 1 1' specify adenine to be colored with RGB triple 0 1 1 (aqua/cyan, corresponding to -block-color='A cyan'). More than one identity (bases) can be specified, separated by; (,:, or also works).
Note: within the PyMOL dssrblock plugin, only or: can be used as a separator: comma (,) or semicolon (;) cannot be used as a separator within a PyMOL command argument (thanks to Thomas Holder for drawing this point to my attention). Case does not matter when specifying id or color. So either ‘A’ or ‘a’, and ‘blue’ or ‘Blue’ or ‘ BLUE’ can be used to make adenine blue: -block-color='a blue'. Some example usages While the above description may appears to be quite complicated, the actual usage of the -block-color option is very straightforward. As always, the cases are best made with concrete examples, as shown below using the classic Dickerson B- DNA dodecamer. # all bases in blue x3dna-dssr -i=355d.pdb -cartoon-block=orient -block-color='N blue' -o=355d-all-blue.pml # # all WC-pairs in red, with the minor-groove edge in 'dim gary' x3dna-dssr -i=355d.pdb -cartoon-block=orient -block-color='wc-pair red; minor dim gray' -o=355d-pair-minor.pml # # thymine (T) in purple, and the upper (+z) face in white # see Figure below, which shows the two bases in WC-pairs are anti-parallel x3dna-dssr -i=355d.pdb -cartoon-block=orient -block-color='T purple; upper 1' -o=355d-T-upper.pml.
Recently I read the article titled by Krauss et al. I quickly ran DSSR on the corresponding PDB entry is. Not surprisingly, DSSR can automatically identify reported key structural features (see output file for details), including the TAT triplet at the quadruplex−duplex junction, and the three G-quartets.
Note that the result is based on biological assembly 1 in PDB file 5dww.pdb1 since the asymmetric unit contains four such molecules. List of 4 multiplets 1 nts=3 TAT 1:A.DT17,1:A.DA19,1:B.DT7 2 nts=4 GGGG 1:A.DG1,1:A.DG5,1:A.DG9,1:A.DG14 3 nts=4 GGGG 1:A.DG2,1:A.DG6,1:A.DG10,1:A.DG15 4 nts=4 GGGG 1:A.DG3,1:A.DG7,1:A.DG11,1:A.DG16 As its title suggests, however, this blog post is about the cartoon-block representations.
Four styles of such schematics are shown below, which can all be easily generated using DSSR/PyMOL. In default style with base-pair blocks minor-groove highlighted top-face highlighted The cartoon-block representations possess unique features not seen elsewhere. With the help of the in PyMOL, they are extremely easy to generate. Such schematics are likely to become popular in illustrations of nucleic acid structures. Over the past couple of years, one of the most significant achievements of DSSR has been its integration into Jmol and PyMOL, two widely used molecular graphics programs.
None of the projects had been ‘ planned’, and I am honored to have the opportunities collaborating directly with Bob Hanson (Jmol) and Thomas Holder (PyMOL). The integrations make salient features of DSSR readily accessible to the Jmol and PyMOL user communities. Moreover, Jmol and PyMOL take different approaches to interoperate with DSSR, and so far they have employed separate features that the program has to offer. Key features of DSSR DSSR was implemented in strict ANSI C as a self-contained command-line program.
The binaries for common operating systems (Mac OS X, Linux and Windows) are tiny (.
3DNA is a 3D Desktop Enhancer that improves the way you work with Windows and the Web. You can choose from different 3D Add-on Worlds to explore and customize with 100's of themes and skies for an immersive and entertaining desktop. 3DNA works by overlaying the wallpaper area and easily lets you toggle Between your 3D and 2D desktop with the click of your mouse. The 3D Worlds also have toys to Play with and integrated 3D games. You can move around easily, or simply teleport to different areas when you want to launch applications, open folders, speed-surf dozens of Web sites, or play music. Personalize each 3D World by hanging your digital photos on the walls by simply dragging them onto the picture frames. Within each World you have various areas to Create links to your folders, files, and programs.
3DNA will even scan your system to create a custom set of links to get you started. Once you have selected the World you like, you can download additional user-created themes and skies or create your own to share.
The interface is intuitive, and there's an optional Tutorial World that walks you through the product.
Starting from 3DNA v2.1, we have streamlined the download procedure. Users just need to in the 3DNA Forum (which normally takes no more than a few minutes) and then login to see the Downloads section where all released and beta test versions of 3DNA and related programs can be downloaded. Moreover, with the same registration, users can post 3DNA-related questions directly in the Forum. To re-emphasize, you must and log in to see the Download section (see the screenshot below), and then click.
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to download 3DNA and related programs; specifically, command-line tools such as wget and curl are blocked on purpose. This page is for instructional purposes only; it does not contain active download links. I strive to continuously improve and extend 3DNA's functionalities for real-world applications. Your comments, suggestions, and bug reports are more than appreciated - I take careful note of each user feedback. Please be aware that for the benefit of the 3DNA-user community at large, I do not provide private email/personal message support; the Forum has been created specifically for open discussions of all 3DNA-related issues. In other words, any 3DNA-associated questions are welcome and should be directed here. Specifically, please do not be shy in sharing openly and concretely any difficult/negative experiences you may have in installing or using the software.
VII The Debug Room is an area within Final Fantasy VII meant exclusively for the game. Final fantasy 16. After dressing as a girl the player can no longer go in, and after the events in Don Corneo's mansion the Honey Bee Inn owners no longer let. The room had a TV screen that displays different locations from Final Fantasy VII: the Sector 5 Church, Cosmo Canyon, Gold Saucer,. Wall Market is a large town-like area made up of two subsections - the northern area and the southern area. He will explain that Tifa is the newest girl and that she has been taken to Don Corneo’s mansion. Don Corneo’s mansion is located in the northern-most part of Wall Market.
Presumably, I've made the message simple and clear enough to get across without further explanation. See also the FAQ entry '. By asking your questions on the public 3DNA Forum, you are benefiting not only yourself but also the user community. I monitor the Forum regularly and respond to posts promptly - browsing the Forum should convince you of my dedication to 3DNA.
Xiang-Jun Here is a list of the current and previously released versions of 3DNA and related programs (DSSR, SNAP, SCHNAaP/SCHNArP). DSSR v1.7.3-2017dec26 ( introducing a new module for the analysis of G-quadruplexes) - DSSR is an integrated software tool for dissecting the spatial structure of RNA. The program has been designed from the ground up to make RNA structure analyses straightforward: it is self-contained and self-explanatory, thus easy to install and simple to use. Give DSSR a try, you may well end up liking it! See my blog post titled ' for more info. Check to give it a try. Log in and to see the active download page.
SNAP beta-r14-2018jan05 - SNAP is a software program for the characterization of three-dimensional Structures of Nucleic Acid-Protein complexes, currently in beta testing release, but fully functional. It shares the same codebase as DSSR. 3DNA v2.3.2-2017dec26 (with C source code) -.
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Log in and to see the active download page. Follow the instructions on ' and post back any questions you may have. 3DNA release v2.0 (with C source code) - accompanying the 2008 Nature Proto cols paper. 3DNA release v1.5 (obsolete) (with C source code) - no longer supported. (with C source code) - this package is a bit aged in applicability, but the algorithms implemented there are straightforward, easy to understand, and still valid.
Miscellaneous Topics related to the 3DNA (2013) JoVE article Moderator: 4 Posts 4 Topics Last post by in on August 12, 2013, 11:07:55 am Background information and technical details on the standard base reference frame. 9 Posts 3 Topics Last post by in on April 02, 2017, 12:53:48 pm Users' contributed scripts, utility programs or recipes related to 3DNA 11 Posts 7 Topics Last post by in on November 25, 2013, 01:58:57 pm Other software, websites, databases, or comments related to 3DNA 34 Posts 11 Topics Last post by in on February 05, 2014, 01:21:46 am SCHNAaP/SCHNArP and CEHS for double helices 20 Posts 5 Topics Last post by in on July 27, 2015, 12:20:05 pm.
Written By Hugo B If you want to customize your desktop in a very original way, this could be the best option. 3DNA Desktop will bring to your computer a 3D world with a different display of your icons, content, and images. With this application, you will get the best of your graphic card. The application completely transforms your desktop into a 3D environment and hundreds of themes to choose from. There are different patterns to choose. A nice house, the inside of a space ship, a museum, and many others.
Just select the place where you feel more comfortable and that will become the world in which you will get in every time you turn on your computer. There, you will place the icons to specific places where they perfectly fit. Besides, 3DNA Desktop has a simple and intuitive interface that will easy up the process. Even that, you must know that you will need some practice to make the 3D creations.