www.archive-org-2014.com » ORG » Y » YASARA

Choose link from "Titles, links and description words view":

Or switch to "Titles and links view".

    Archived pages: 147 . Archive date: 2014-06.

  • Title: YASARA - Yet Another Scientific Artificial Reality Application
    Descriptive info: .. What does YASARA look like?.. Click here to visit the OpenGL screenshot gallery.. Click here for instant download!.. NEW:.. YASARA for Android brings the most feature-complete molecular modeling environment to selected smartphones and tablets, including interactive molecular dynamics simulations.. WELCOME TO.. About YASARA - Watching Nature@Work.. YASARA is a molecular-graphics, -modeling and -simulation program for Windows, Linux, Mac OS X and.. Android.. developed since 1993, that finally makes it really easy to answer your questions.. With an.. intuitive user interface, photorealistic graphics.. and support for affordable.. shutter glasses.. ,.. autostereoscopic displays.. and.. input devices.. , YASARA creates.. a new level of interaction with the 'artificial reality'.. , that allows you to focus on your goal and forget about the details of the program.. YASARA is powered by PVL (Portable Vector Language), a new development framework that provides.. performance way above traditional software.. PVL allows you to visualize even the largest proteins and enables true interactive real-time simulations with highly accurate force fields on standard PCs (.. see benchmarks.. ).. You can push and pull molecules around and work with dynamic models instead of static pictures.. Being rooted in the academic world, all methods introduced by YASARA are.. described in peer-reviewed journals.. You can obtain the initial stage '.. YASARA View.. ' for free, while higher stages (.. YASARA Model.. YASARA Dynamics.. YASARA Structure.. ) require a.. license fee.. that allows us to guarantee new developments, updates and support also in the future, independent of temporary grants.. As a YASARA user, you are not limited to  ...   NOVA.. pH dependent typing of organic molecules.. Fastest molecular dynamics algorithms, see benchmarks.. MD simulation of membrane proteins with 4 clicks.. Automatic force field parameter assignment for 98% of the PDB.. Yanaconda macros.. and Python scripts.. Homology modeling with 4 clicks.. CASP approval.. Small-molecule docking with 4 clicks.. Modeling and simulation on smartphones and tablets.. Side-chain prediction.. pH dependent hydrogen bonding networks.. Structure validation including ligands.. NMR structure determination with 4 clicks.. Multi-dimensional knowledge-based potentials.. WHAT IF YASARA knows the answer?!.. With over 2000 citations,.. WHAT IF.. is a widely used modeling program, well known e.. g.. for its structure validation and prediction tools.. The.. WHAT IF / YASARA Twinset.. is a unified all-in-one distribution of the two programs with extended functionality.. If you run the Twinset WHAT IF, an additional YASARA menu provides quick access to molecular simulations.. And vice versa, users of the Twinset YASARA can simply run WHAT IF commands, so that WHAT IF inherits YASARA's user interface, graphics engine, macro language and convenience functions like unlimited undo/redo.. This approach makes WHAT IF quickly accessible, also to users outside the bioinformatics expert community.. Acknowledgements.. : YASARA would not exist in its present form without the support of: Prof.. Dr.. Gregor Hoegenauer (Institute for Molecular biology, Biochemistry and Microbiology,.. IMBM.. , University of Graz, Austria), Prof.. Guenther Koraimann (.. Andreas Kungl.. (Institute for Pharmaceutical Chemistry.. Gert Vriend (.. CMBI.. , University of Nijmegen, the Netherlands).. YASARA is a molecular graphics, modeling and simulation program for Linux, Windows and Mac OS X, (C)1993-2014 by Elmar Krieger..

    Original link path: /
    Open archive

  • Title: YASARA - Products
    Descriptive info: Products.. There are four different stages of YASARA for.. Linux, Windows, Mac OS X.. , aimed at increasingly complicated fields of application.. A certain stage contains the features of all the previous stages, plus a number of additional functions to tackle a wider range of scientific questions.. Features with unique properties.. which you will not find in other programs are marked with orange buckyballs below.. - Molecular graphics and analysis,.. freely download now.. - Everything above, plus molecular modeling.. - Everything above, plus molecular simulations.. - Everything above, plus structure prediction and validation, docking, knowledge-based potentials.. YASARA NMR Module.. - NMR structure determination.. YASARA/WHAT IF Twinset.. - Extensive structure validation (PDBReports) and WHAT IF functions.. Android tablets and smartphones that can run interactive MD simulations starting at 199 EUR.. A stereoscopic molecular modeling lab for 250 EUR.. , and a.. cave for 700 EUR.. Read more about.. the philosophy behind YASARA.. System requirements.. : None, please download the free YASARA View to verify that YASARA runs on your computer (and.. please contact us.. if you encounter problems).. Stage I: YASARA View - Free download.. is available for free and contains all the functions you need to explore a macromolecular structure interactively.. As a bonus, you get YASARA's innovative 3D engine, which is up to 35 times faster than what you usually know from.. OpenGL.. (.. ), you can load multiple structures at the same time, create publication-quality ray-traced images including labels, and program your own macros and Python plugins.. Included is.. YASARA Movie,.. a player for multimedia presentations and tutorials created with any of the higher stages, as well as the.. YASARA Python module.. to simply 'import yasara' in your Python scripts.. Key features:.. Cross-platform and easy installation:.. Windows, Linux and Mac OS X in the same directory, run directly from USB stick.. Photo-realistic molecular graphics with full-scene antialiasing:.. up to 35 times faster than other OpenGL based solutions.. , even the ribosome rotates smoothly in CPK mode.. Support for the latest GPU shader features like hardware tessellation, where the GPU increases the geometric details of polygon meshes (e.. surfaces and secondary structure).. Parallel (orthographic) and perspective projection.. Interactive.. box, freehand/lasso or sphere selection tools.. Support for over 70 molecular fileformats (based on OpenBabel).. Download PDB files from the RCSB or.. the re-refined and improved version from PDB_REDO.. Optimal depth perception thanks to.. real-time shadows and ambient lighting, even on older hardware.. All common graphics styles:.. CPK.. balls sticks.. sticks.. traces.. tubes.. ribbons.. cartoons.. labels.. arrows.. Interactive secondary structure morpher, which seamlessly interpolates between a realistic (close to Calpha) and an idealistic (perfectly straight strands and helices) secondary structure display, which can additionally be configured in countless ways to match your favorite secondary structure styling.. Ray-tracing for publication quality graphics.. at arbitrary resolutions, interactively move the lightsource, adjust shadows.. Color any PDB file by sequence conservation and quality indicators (automatically mapped from HSSP/PDBFinder2).. Superpose structures and structure ensembles, calculate proper RMSDs.. (minimized by flipping equivalent atoms).. Align multiple proteins based on their structure or sequence.. , using a variety of methods.. Identify related structures in the PDB.. Measure distances, angles, dihedrals.. Build.. atoms, residues, peptide chains and mutate amino acids.. Visualize.. contacts.. hydrogen bonds.. , and.. hydrophobic.. /.. pi-pi.. cation-pi interactions.. Create realistic.. 3D structures from nonsense, 1D or 2D molecules.. convert them back to 2D structural formulas.. Automatic assignment of.. fractional bond orders.. and missing hydrogen atoms,.. graph-theory based typing of hetero-polycycles.. Analyze and change atomic B-factors and occupancies, rename and renumber atoms and residues.. Extremely fast algorithms to show and update.. Van der Waals, molecular and solvent accessible surfaces.. in real-time.. Extend YASARA with your.. own functions using the Python scripting language.. Use YASARA from your Python scripts, simply 'import yasara'.. Simple.. Yanaconda macro language.. to automate your work and create flexible animations.. eLearning functions:.. interactive tutorials.. provide the knowledge about molecular structure, modeling and simulations.. Click here for free download.. click here for screenshots.. click here for a complete feature list.. Stage II: YASARA Model.. contains YASARA View and adds all the functions you need to explore, analyze and model small to macromolecules in a production environment.. This includes many features you often miss: unlimited undo/redo, macro recorder, quad-buffered stereo with.. or.. stereoscopic screens.. You can load thousands of structures at the same time, move them around independently and create multimedia presentations (YASARA Movies).. These movies can be encoded as MPEGs and pasted into Powerpoint or played back with all stages of YASARA, including the free YASARA View.. All the features of YASARA View listed above are included, no need to keep a separate YASARA View installation.. Fully immersive OpenGL 3D stereo graphics with.. sterescopic screens.. High quality GPU accelerated anaglyph stereo mode for red/cyan glasses, that tricks the brain into seeing full color and enables stereo also on notebooks.. Red/cyan glasses are included.. Create the.. fanciest molecular animations.. with automatic rotations, movements, zooms,.. text in 3D letters.. texture mapping of PNG/JPG images.. conversion to 3D objects.. Encode animations in MPEG format, paste them into Powerpoint presentations.. Export Alias Wavefront objects for use by 3DStudioMax and others.. Import OpenOffice Impress and Microsoft Powerpoint presentations, add molecular animations to the slides.. Work with thousands of structures at the same time, move them around independently.. Extensive coordinate manipulation: center, join, transform, oligomerize,.. transfer fragments (e.. loops).. replicate them (e.. domains).. Analyze contacts, hydrogen bonds, hydrophobic/pi-pi/cation-pi interactions and protein secondary structure.. Align small molecules like ligands automatically, by.. superposing them on the largest common fragment.. Measure distances, angles and dihedrals between groups of atoms like helices or planar side-chains.. Change distances, angles and dihedrals interactively.. Choose a default pH from 0 to 14 when.. assigning fractional bond orders and adding hydrogens.. Show and calculate.. , distinguish between.. outer and inner surfaces.. , calculate volumes.. Analyze and show cavities formed by these surfaces.. Create multiple interactive cut-planes.. to look inside surfaces and other objects.. Identify cis-peptide bonds and wrong stereoisomeres.. Store the results of your analysis in tables, import them in Excel.. Record macros or write them with a text editor.. Support for special input devices like SpaceBall and P5 glove (currently Linux only).. Unlimited undo/redo.. YASARA Model costs 110 / 148 $ for academic and 550 / 742 $ for commercial use, including one year of support and updates.. This price includes Windows, Linux and.. Mac OS X costs 20% extra.. , red/cyan stereo glasses and shipping are included, customers in Austria have to add 20% VAT.. Click here to order or get a quotation.. click here for license details.. Stage III: YASARA Dynamics.. contains YASARA Model and adds support for molecular simulations.. In addition to YASARA's own force fields (.. ) you can use other well known MD force fields like AMBER, and run accurate all-atom MD simulations in aqueous solution with Particle Mesh Ewald longrange electrostatics at twice the speed you know from other programs.. is not a "black box" with input and output files, but shows the MD simulation in real-time on screen.. You can fully interact with the scene, pull atoms or whole molecules around and finally do the type of molecular modeling that Cyrus Levinthal  ...   20% VAT.. To order the Twinset, just place a.. normal order for YASARA Dynamics.. and then request the Twinset upgrade from.. , telling us your WHAT IF license number.. If you already own YASARA, email us your YASARA serial number and WHAT IF license number.. Molecular modeling on Android for 175 EUR.. Since April 2013, YASARA is available for selected Android smartphones and tablets,.. providing today's most feature-complete mobile molecular modeling environment, including interactive MD simulations.. Tablet prices start at 175 EUR,.. two videos and all the details are available here.. The 3D Molecular Modeling Lab for 250 EUR.. Stereoscopic 3D molecular modeling hardware.. has become easily affordable, so that entire classrooms can enjoy this unique experience.. The image on the right shows the easiest and cheapest solution: 3D vision is provided using 'passive stereo', where the images for left and right eye are shown in odd and even pixel lines and separated using flicker-free polarized glasses.. The first popular screens with this feature were the Zalman ZM-M215W, ZM-M220W and ZM-M240W, costing around 200 EUR.. Unfortunately it appears that Zalman discontinued this product line, so they are now mostly available as refurbished second hand models.. But there are many follow up products, googling for.. passive stereo odd even.. finds e.. the LG D2342P, the HP 2311x, the AOC e2352Phz or the Viewsonic V3D231.. The big advantage is that this type of display is directly supported by YASARA with.. any.. graphics card and.. operating system (no expensive Quadro/FireGL cards or special video drivers are needed).. You can move your molecules through 3D space using the.. Connexion 3D SpaceNavigator.. with six degrees of freedom.. Order now for 50 EUR.. Notes:.. The ZM-M220W has a resolution of 1680x1050 pixels.. The polarized glasses ensure that the left eye sees only the odd pixel lines, while the right eye sees the even lines.. So the resolution is reduced to 1680x525 pixels per eye as soon as the glasses are put on.. This is hardly noticeable when looking at molecules, but becomes apparent when looking at characters.. Text is therefore harder to read than with alternative, more expensive stereo solutions.. Without glasses, the screen behaves just like any other screen and can be used for everyday work.. It has a quite glossy surface, reflections can be a problem in bright rooms, but are hardly noticeable in somewhat darker 'molecular modeling caves'.. At least YASARA Model is required.. High Resolution 3D Modeling for 350 EUR.. High resolution 3D stereo with shutter glasses.. is the next higher level, since it does not suffer from the reduced resolution of the Zalman screens above.. The probably easiest solution with the best price/performance ratio is the.. Viewsonic V3D241wm.. shown on the right.. The screen with a 24"/60cm diagonal has a resolution of 1920x1080 pixels and a non-reflective surface, it is thus well suited for everyday work.. It functions with every operating system and every graphics card (nVIDIA/AMD) that can display quad-buffered stereo with 100 or 120Hz at a resolution of 1920x1080 pixels.. The shutter glasses are included in the 350 EUR package.. A slightly more expensive but also more commonly used and more flexible solution is.. nVIDIA's 3D Vision system.. , check the guidelines.. here.. Other suppliers of 3D glasses are.. eDimensional.. RealD.. Your graphics card must have a dual-link DVI connector and support quad buffered OpenGL stereo, a feature which is normally only available in.. workstation products like nVIDIA Quadro.. and AMD FireGL.. You do not need the very expensive high-end Quadros with mini-DIN stereo connector, since the shutter glasses are supplied with the screen and plug into the screen with a cable, neither emitter nor batteries are required.. Only one pair of glasses can be connected, so this system is for one person only.. And since the monitor does not know the difference between left and right image, you may have to swap left and right in YASARA on startup.. The aspect ratio of 16:9 is very movie-like, you may have to fiddle with your desktop settings to avoid windows that are too wide to read.. The screen shows very little ghosting, which becomes noticeable mainly in the bottom 5cm.. The 3D Molecular Modeling Cave for 700 EUR.. Recently also.. specialized 3D beamers.. , that previously cost above 10000 EUR, have finally become mainstream technology.. You can now easily build your private molecular modeling showroom, projecting giant 3D views that measure several meters along the diagonal.. The image on the right shows a 3D beamer from Viewsonic, costing around 500 EUR.. The beamer projects the images for left and right eye alternatingly with 120 Hz.. So you additionally need shutter glasses to separate the images, the probably best choice are glasses with DLP-link like the.. Viewsonic PGD-250.. (~80 EUR) or the.. XPAND Edux3.. (~80 EUR).. An alternative with a less comfortable infrared emitter are the.. nuVisionGX glasses.. shown on the right (~200 EUR).. Any beamer that is 3D-ready, features 'DLP-link' and supports a 120 Hz mode over VGA or DVI cable should work with YASARA, to see examples.. click here.. , then select 'Supported 3D projectors'.. Tests have been done in Linux, where you need to add a 120Hz modeline to your xorg.. conf.. Other operating systems work too if they allow you to choose a 120Hz video mode in their display settings.. Additionally, your graphics card must support quad buffered OpenGL stereo, a feature which is normally only available in.. These cards often also have a mini-DIN connector for the shutter glasses, which is however not needed if you chose glasses with DLP-link (see above).. The only disadvantage of DLP-link glasses is that you sometimes need to manually flip left and right image.. At least YASARA Model is required to display stereo.. DTI Virtual Window.. The Virtual Window.. is an autostereoscopic 19" LCD/TFT screen that allows you to see 3D without any additional glasses.. Just press a button to switch between 3D and 2D mode.. Order now from.. Dimension Technologies.. The Virtual Window provides a 3D button, that activates a filter which directs the odd pixel columns to the left eye, and the even pixel columns to the right eye.. So the original resolution of 1280x1024 pixels is reduced to 640x1024 pixels per eye, leading to reduced text quality, just like the Zalman screen above.. Since there are no glasses, the 3D view depends on your position and inverts if the head is moved too far.. The Virtual Window requires at least YASARA Model and a video card that supports quad-buffered OpenGL stereo, e.. NVIDIA Quadro cards.. The Models@Home Cluster System.. Models@Home.. is a distributed computing environment that follows the spirit of the famous.. Seti@Home.. project, but is not tied to a specific application.. Instead you can run all your favourite programs in parallel, without any need to modify or adapt them.. The Models@Home screensaver allows to turn a heterogeneous Windows / Linux network into a uniform cluster.. At the.. , Models@Home is used for most protein modeling tasks, all YASARA force fields were developed with computer power provided by Models@Home.. Models@Home is freely available including the source code.. Click here to download.. click here for more information..

    Original link path: /products.htm
    Open archive

  • Title: YASARA - Download Center
    Descriptive info: Download Center.. What do you want to download?.. YASARA for new users.. If you have not used YASARA before,.. to register and obtain YASARA.. Also.. if you want to upgrade to a higher YASARA stage.. YASARA for registered users.. If you have already used YASARA before,.. to download YASARA again or update to version 14.. 6.. 5.. If you want to know what is new,.. visit the  ...   a problem to solve, visit the YASARA repository.. Someone else may already have provided the solution.. to access the repository.. If you want to get a cluster for free,.. install the Models@Home screensaver.. and run your programs in parallel.. Structural Bioinformatics Tools.. If you are working in structural bioinformatics,.. look at our collection of useful programs.. that will make your life easier.. Licensed under the GNU GPL..

    Original link path: /downloads.htm
    Open archive

  • Title: YASARA - News
    Descriptive info: YASARA News.. Please choose a news topic.. Scientific News.. If you want to see examples how YASARA is used to answer scientific questions,.. Development News.. If you want to know about the latest YASARA developments,.. click here for the major highlights.. here for all new functions.. YASARA in press.. A list of papers involving YASARA is.. available here.. Please.. send us the reference.. if you published work supported by YASARA..

    Original link path: /news.htm
    Open archive

  • Title: YASARA - Contact, Support and Mailing Lists
    Descriptive info: Contact, support and mailing lists.. If none of the options below fit your needs, just email us:.. What do you want to do?.. (If you are just looking for more information about us,.. ).. Report a problem or inconvenience and get it fixed.. If you encountered a problem, bug or inconvenience that annoys you, please.. report it here.. and receive an update plus up to 10 / 14 $ for your help.. Contribute movies, plugins, macros or other source code.. If you want to share your developments with other users,.. to submit them to the YASARA Repository.. Of course you will be paid for your contribution, the maximum amount being equal to a  ...   second YASARA account.. for support.. Request a copy of your personal data.. If there is anything you want to know or check about your YASARA license account,.. to request a copy of all the information we have stored in our database.. Change your email address.. Most of the contact options require that you enter the same email address as during your initial registration.. Click here to change this address.. Request a new feature.. If you are missing an essential feature,.. please notify us.. Especially if the absence of the feature makes you reconsider using YASARA in the future.. Make personal contact.. If none of the options above fit your request,.. to contact us directly..

    Original link path: /contact.htm
    Open archive

  • Title: YASARA - Yet Another Scientific Artificial Reality Application
    Descriptive info: About us.. is brought to you by.. YASARA Biosciences.. in close collaboration with the.. WHAT IF Foundation.. Spronk NMR Consultancy.. Our final goal is to advance science by providing the community with the required research tools.. WHAT IF and YASARA are aimed at becoming an all-in-one solution that takes the steps from protein sequence to structure to function to drug design, and is nevertheless powerful enough to handle the large amounts of data required by structural and functional genomics projects.. Due to the enormous size of the problem, collaborations with other research groups are always welcome.. We generally use scientific results instead of sales-departments to convince our customers.. This approach saves a lot of money, which in turn allows us to offer the software for free or at realistic, non-fantasy prices (depending on the product), for academic as well as industrial environments.. Any new methods used in our programs are.. published in peer-reviewed journals.. , so that you never have to rely on brochures instead of scientific facts.. By obtaining software directly out of the research lab, you can be sure not to waste money on a program whose development essentially stopped five years ago - far too long in this rapidly evolving field.. If you want to contact us,.. just click here.. Development of YASARA was started in 1993 by.. Elmar Krieger.. , together with his study of Molecular Biology at the University of Graz, Austria.. In 1997, YASARA became the topic of his master's thesis, supervised by Prof.. Günther Koraimann.. In 2000, YASARA moved to the Center for Molecular and Biomolecular Informatics (CMBI) in Nijmegen, the Netherlands, where Elmar became PhD student of Prof.. Gert Vriend.. In 2002, Elmar founded YASARA Biosciences, a company located in  ...   years as software architect at BOC Information Systems in Vienna), to OpenGL graphics programming and general GPU computing.. In 2007, he was among the first to publish an article about the implementation of a complete molecular dynamics algorithm on the graphics card using CUDA.. started programming WHAT IF in 1987 as a PostDoc in Groningen, the Netherlands.. In 1989, he moved to the EMBL in Heidelberg, joining the group of Chris Sander.. From 1996 on, he led the 'Vriend group' and, together with his students, added an uncountable number of options to the program.. Since 2000, he is 'Professor of Bioinformatics' and head of the Center for Molecular and Biomolecular Informatics (CMBI) in Nijmegen, the Netherlands.. Elmar Krieger (on the left) was his first PhD student there.. The WHAT IF Foundation is a non-profit organization founded in 1992, that uses revenues from WHAT IF sales to ensure further WHAT IF development and to support students.. Chris Spronk.. graduated in biophysical chemistry and biochemistry at the Radboud University in Nijmegen, The Netherlands.. He then specialized in biomolecular NMR spectroscopy, as well as method development in structure refinement validation during subsequent PhD and post-doctoral research periods at the Department of NMR-spectroscopy (Utrecht University), the Department of Biophysical Chemistry and the Center for Molecular and Biomolecular Informatics (Radboud University in Nijmegen).. In 2006 he founded Spronk NMR Consultancy to provide his experience to partners from academia and industry.. Contact address:.. YASARA Biosciences GmbH.. Elmar Krieger.. Wagramer Strasse 25/3/45.. 1220 Vienna.. Austria / Europe.. VAT-Number: ATU65614837.. www.. yasara.. org.. WHAT IF Foundation / CMBI.. Prof.. Gert Vriend.. Toernooiveld 1.. 6525 ED Nijmegen.. The Netherlands.. VAT-Number: NL003634255B02.. cmbi.. ru.. nl/whatif.. Spronk NMR Consultency.. Chris Spronk.. Pylimo gatv 6.. LT-01117, Vilnius.. Lithuania.. spronknmr.. eu..

    Original link path: /about.htm
    Open archive

  • Title: YASARA Screenshots
    Descriptive info: YASARA Screenshots.. In addition to the ray-traced images shown here, there are also direct screenshots of the YASARA window available.. YASARA's look across the various operating systems.. Examples for real-time shadows and ambient lighting.. YASARA movies.. YASARA command examples..

    Original link path: /raytrace.htm
    Open archive

  • Title: YASARA View - Download
    Descriptive info: Download.. Note:.. If you already downloaded YASARA once, don't do it again, but.. request an update instead.. Please customize your free personal edition of.. Your operating system:.. Windows.. Linux.. Mac OS X (Intel CPU only, YASARA is not available for PowerPC).. Android (Intel CPU only, YASARA is not available for ARM).. Windows & Linux, install and update from Windows.. Linux & Windows, install and update from Linux.. Mac OS X & Linux, update from Mac OS X.. Mac OS X & Windows, update from Mac OS X.. Mac OS X, Linux & Windows, update from Mac OS X.. Your processor:.. Include support for all processors, please keep this  ...   Nehalem/Westmere).. 1 (2007, e.. Intel Penryn).. (S)SSE3 (2006, e.. Intel Core, Intel Atom, AMD Bobcat).. SSE3 (2004, e.. Intel Pentium 4 Prescott, AMD Phenom).. SSE2 (2001, e.. Intel Pentium 4, AMD Athlon 64).. SSE (1999, e.. Pentium 3, Athlon XP, only View+Model).. Please use only plain English characters in the fields below.. Your first name:.. Your middle initials:.. (optional).. Your family name:.. (optional but appreciated).. Department:.. University/Company:.. Download link will be sent there.. Please doublecheck the email address, it is essential for downloads, updates and support.. YASARA is linked with the.. Simple Direct Media Layer library.. which is released under the GNU LPGL.. Click here for LGPL compliance information..

    Original link path: /viewdl.htm
    Open archive

  • Title: YASARA for Android
    Descriptive info: YASARA for Android.. Download now from Google Play Store.. Time is always short in science, and consequently a major focus during YASARA development has always been to deliver your results as quickly as possible.. This goal could be achieved by using PVL, YASARA's custom vector language, that employs MMX/SSE/AVX assembler code.. to deliver a 2x-4x performance advantage.. over normal C/C++ applications.. In 2012, it has finally become possible to carry this performance advantage along to a different world - the world of Android smartphones and tablets.. The credit goes to Intel, who released the Medfield 'system on a chip' (.. in-depth review available here.. ), that empowers smartphones and tablets to execute not only traditional Android apps, but also YASARA's highly optimized MMX/SSE assembler code.. Medfield and its built-in PowerVR GPU are even fast enough to run YASARA '.. as it is.. ', so you do.. not.. get a stripped down app that just happens to share the name with the desktop version, but everything works exactly as you know and expect it, making YASARA the most feature-complete molecular modeling software for smartphones and tablets.. Watch the video on the right to see how we tuned the user interface to guarantee an enjoyable experience also on tiny smartphone screens.. YASARA for Android has been released in April 2013, and requires.. an Intel-inside smartphone or tablet.. If you own an iPhone/iPad,.. please look here for details.. If you are just about to buy yourself a new gadget, consider to choose one from the list below.. There is no extra charge for YASARA on Android.. Intel-inside Android smartphones that can run YASARA:.. Motorola Razr i.. (see video on the upper right): distributed in many countries and therefore easy to obtain,.. e.. from Expansys.. , has been used to port YASARA to Android and has the fastest CPU (2GHz).. It is  ...   RAM, 16GB storage and Android 4.. 0.. can be ordered from us or directly from the manufacturer.. This was the first Android tablet that could run YASARA, with half the CPU power of the Samsung Galaxy Tab 3 above.. Asus FonePad.. : 7" tablet, which is actually a "phablet", since it also works as a mobile phone.. More details at the Asus website.. Asus MeMO Pad FHD 10.. : The resolution of its full HD display is probably too high to be convenient (slows down the graphics since more pixels need to be calculated, some text will be too small).. The following limitations currently apply to YASARA for Android:.. Only the free YASARA View is available from the Google Play store,.. YASARA Model and YASARA Dynamics must be purchased and downloaded from here.. YASARA Structure is currently not available for Android and will probably have to wait until Smartphones with 2 GB RAM are released (Windows 8 tablets have all 2 GB RAM,.. so YASARA Structure runs fine there.. Python plugins are not yet supported.. Ray-tracing with POV-Ray is not possible, since there is no POV-Ray for Android.. But you can save POV-Ray scenes.. The video above shows YASARA running on the.. smartphone, including a molecular dynamics simulation with explicit solvent.. It also gives some general background information about YASARA on Android.. Detailed usage instructions can be found in the second video further below.. , available in India.. , distributed worldwide.. Orange San Diego,.. available in France and the UK.. Ramos W32 tablet.. , providing general YASARA usage instructions and an example for coloring protein surfaces by electrostatic potential using a Poisson-Boltzmann calculation.. Everything works exactly the same on smartphones.. Many thanks to.. Steven Martin.. for guiding through the movies.. The tablet above is the.. Ramos W32, the world's first Intel-inside tablet.. , costing around 200 / 270 $..

    Original link path: /android.htm
    Open archive

  • Title: Why YASARA?
    Descriptive info: Why YASARA?.. Back in 1966, Cyrus Levinthal (known even to first-year biochemistry students thanks to the "Levinthal Paradox" of protein folding) published a clairvoyant article in Scientific American (fig.. 3) that marks the official beginning of molecular graphics and interactive modeling.. Having pointed out the importance of true interaction between the user and the program during modeling (".. it is our experience that an investigator, who is looking at a molecule can frequently understand the reason for a local minimum and by making a small alteration in the structure can return the program to its downhill path.. "), he concluded that by adding pseudo-energy terms to the molecular dynamics force field, we can ".. do the same pulling and pushing in the computer that we can do with our hands while building actual models.. ".. Nevertheless, his ideas have not really made it into todays modeling and molecular dynamics programs.. If you want to know if an Aspartate and a Lysine on the protein surface can form a salt-bridge, you are still often asked to change torsion angles - would it not  ...   whole scene in 3D with.. or a.. stereoscopic TFT screen.. If it is useful - then why do not all modeling programs allow you to do that? The reason is simple: displaying a large protein including surrounding water molecules while running a molecular dynamics simulation - that is still at the edge of what is possible on a single PC today, even with a 3.. 2 GHz CPU.. YASARA therefore makes extensive use of PVL (Portable Vector Language), a new approach to portable high performance computing.. PVL allows us to guarantee highest performance and accuracy.. Check the benchmark page for details.. Fig.. 1: The official start of molecular graphics - back in 1966 at the M.. I.. T.. More details can be found at the.. Max-Planck Institute for the History of Science.. 2: The first YASARA workstation in 1997: Pentium 133, shutter glasses, ultrasonic pointer, virtual reality helmet and force feedback joystick with six degrees of freedom.. 3: Cyrus Levinthal's clairvoyant article from 1966 - most of it is even more valid today than back in these early times of molecular modeling..

    Original link path: /why.htm
    Open archive

  • Title: The YASARA Benchmarks
    Descriptive info: The YASARA Benchmarks.. Since the first YASARA website went online in 1999, we have been providing benchmarks to allow an objective comparison with other programs.. Our goal is however.. to start 'benchmark wars' with other groups, as we are all trying to solve the same problems.. So instead of comparing other programs with YASARA directly, we offer symbolic rewards of 100$ for the first one who can beat YASARA in one of the following benchmarks.. (You do not have to use your own program, just anything you find).. The following restrictions apply:.. Benchmarks are shown for one or more combinations of CPU model, RAM and graphics card.. Your program must be faster on the same or a slower PC.. Your program must be available, you must be able to reproduce your results.. Only the first one who wins a benchmark gets the reward, then the benchmark will be removed.. Benchmark 1:.. 100$.. for a faster molecular dynamics algorithm.. The image on the right shows a classic molecular dynamics benchmark: dihydrofolate reductase (PDB entry 1AOE) and 6875 water molecules, summing up to 23788 atoms.. You can.. download the PDB file here.. Here we measure the time required for one full simulation step of a standard MD protocol using the AMBER03 force field and TIP3P water:.. Find the neighbors within a 7.. 86 Å cutoff distance (usually via a grid-based search).. Calculate the intramolecular (bonds, angles, dihedrals) and shortrange intermolecular (Coulomb, VdW) forces, including the PME shortrange damping function.. Calculate the longrange electrostatic forces using the PME algorithm: interpolate the charges on a grid with 1 Å spacing and 4th order B-splines, perform the two fast fourier transforms and convolution, subtract the longrange component from bonded intraaction partners.. Integrate the equations of motion and move the atoms one step further.. Here are the execution times on various CPU types (single-core only, see next benchmark for multi-core performance).. In our hands, especially the SSE4.. 1 code path is about.. 60% faster than the closest competitor.. (measured in 32bit Linux with standard GCC compiler).. CPU model.. Opteron 265.. Core 2 Duo.. Xeon L5420.. Code path.. 3DNow! + SSE + SSE2 + SSE3.. SSE + SSE2 + (S)SSE3.. SSE + SSE2 + (S)SSE3 + SSE 4.. 1.. CPU cycles.. 292.. 91 million.. 231.. 78 million.. 189.. 95 million.. Actual time.. 0.. 1627 seconds @ 1.. 8 GHz.. 1073 seconds @ 2.. 16 GHz.. 07598 seconds @ 2.. 5 GHz.. Notes:.. How the results above translate to.. simulated nanoseconds per day.. depends on the chosen timestep and thus the accuracy/performance tradeoff you are willing to take.. If bonds to hydrogen atoms are constrained and rigid water molecules are used, YASARA reliably reaches a timestep of 4 femtoseconds.. Benchmark  ...   provides a very accurate view of protein structure.. Running a molecular dynamics simulation of such a crystal moves the protein away from where it should be, due to inaccuracies in the force field.. The smaller the damage, the more accurate the force field.. During a 1 nanosecond simulation with YASARA's YAMBER2 force field, the maximum Calpha RMSD from the true structure is 0.. 70 Å.. 100$ are yours if you manage to obtain a lower RMSD with any MD program / force field you like, under the condition that you did not optimize the force field specifically for 2A0B or its homologues.. Hydrogens have been added with WHAT IF's H-bond network optimizer, counter ions and disordered water molecules were placed by YASARA.. The cell size is 30.. 456 x 34.. 924 x 110.. 741 Å, you can.. download a PDB file here.. Simulations must be run at the temperature of experimental structure determination (277K).. Save snapshots in intervals of 5ps and calculate the average Calpha RMSD for all four chains.. This average must stay below 0.. 70 Å in all 200 snapshots to win the benchmark.. Benchmark 4:.. for better molecular graphics.. The screenshots on the left show PDB entry 1N8R, the 50S ribosomal subunit with 98569 atoms, in space-filling mode.. In the upper image, all atoms are on screen, YASARA delivers either 10 frames per second without shadows (many programs are a factor 35 slower), or 5.. 5 frames per second with shadows calculated in real-time (as shown).. On the lower image, we flew right through the ribosome to the backside, most atoms are now off-screen, resulting in 106 frames per second without shadows (as shown).. To win the 100$, your program must be faster in both cases (either with or without shadows), while reaching at least the same visual quality (e.. spheres must be equally round), and it must run on the same or a slower system.. Benchmark system:.. Opteron 265 single-core @ 1.. 8 GHz,.. Window size 1024x768, color depth 32 bits, nVIDIA Geforce 6600 graphics card.. Benchmark 5:.. for faster interactive molecular dynamics.. Interactive molecular modeling during a real-time molecular dynamics simulation allows you to pull individual atom and entire molecules around with the mouse or 3D input devices.. The image on the right shows the simulation of dihydrofolate reductase (see benchmarks 1 and 2 above for details), including all water molecules.. Using four CPU cores on the system described below, YASARA reaches 12 frames per second, i.. 12 molecular dynamics steps and 12 screen updates including real-time shadows.. To win the 100$, your program must be faster on the same or a slower system and reach at least the same visual quality.. Opteron 265, four cores @ 1..

    Original link path: /benchmarks.htm
    Open archive

  • Archived pages: 147