°  General °  Working with YASARA Figure: A snapshot from the movie A tutorial explaining how to work with YASARA to new users. Many thanks to Sven Geier for his 'Planetary' background (more at www.sgeier.net/fractals). Written by: Elmar Krieger License: GNU GPL Last modified: 2013/03/25 Download: http://yasara6.cmbi.ru.nl/welcome.zip °  Working with the Twinset Figure: A snapshot from the movie An introduction to using WHAT IF from within YASARA. Many thanks to Sven Geier for his 'Sigmaspace' background (more at http://www.its.caltech.edu/~sgeier/). Written by: Elmar Krieger License: GNU GPL Last modified: 2013/01/27 Download: http://yasara6.cmbi.ru.nl/twinset.zip °  What's new in YASARA Structure Figure: A snapshot from the movie An overview of the new features in YASARA Structure Written by: Elmar Krieger & James Magahern License: GNU GPL Last modified: 2012/04/01 Download: http://yasara6.cmbi.ru.nl/structure.zip °  Calibrating and using the P5 data glove Figure: A snapshot from the movie This tutorial allows you to calibrate the P5 data glove available from www.EssentialReality.com. Usage instructions are also included. Written by: Elmar Krieger License: GNU GPL Last modified: 2008/07/11 Download: http://yasara6.cmbi.ru.nl/p5.zip °  Molecular graphics °  The Basics Figure: A snapshot from the movie A tutorial explaining how to use YASARA to create ray-traced molecular graphics. Many thanks to Sven Geier for his 'Opalshards' background (more at http://www.its.caltech.edu/~sgeier/). Written by: Elmar Krieger License: GNU GPL Last modified: 2013/01/27 Download: http://yasara6.cmbi.ru.nl/molgra.zip °  Surfaces II - Environments Figure: A snapshot from the movie Written by: Elmar Krieger License: GNU GPL Last modified: 2012/06/03 Download: http://yasara6.cmbi.ru.nl/surfaces2.zip °  Surfaces III - Electrostatics Figure: A snapshot from the movie Written by: Elmar Krieger License: GNU GPL Last modified: 2012/04/01 Download: http://yasara6.cmbi.ru.nl/surfaces3.zip °  Surfaces I - Introduction Figure: A snapshot from the movie An introduction to the different kinds of surfaces. Many thanks to Sven Geier for his 'Speed' background (more at http://www.its.caltech.edu/~sgeier/). Written by: Elmar Krieger License: GNU GPL Last modified: 2012/04/01 Download: http://yasara6.cmbi.ru.nl/surfaces.zip °  Lighting and shadows Figure: A snapshot from the movie An introduction to lighting and shadows in YASARA. Many thanks to Sven Geier for his 'Thetaspace' background (more at http://www.its.caltech.edu/~sgeier/). Written by: Elmar Krieger & Sven Geier License: GNU GPL Last modified: 2012/04/01 Download: http://yasara6.cmbi.ru.nl/lighting.zip °  Advanced GPU effects Figure: A snapshot from the movie A demonstration of the features of YASARA's new GPU shader-based graphics engine Written by: Elmar Krieger and Jacobus van Meel License: GNU GPL Last modified: 2012/04/01 Download: http://yasara6.cmbi.ru.nl/gpueffects.zip °  Cut-planes Figure: A snapshot from the movie A tutorial about using cut-planes to look inside surfaces and other polygon meshes Written by: Elmar Krieger & Sven Geier License: GNU GPL Last modified: 2012/04/01 Download: http://yasara6.cmbi.ru.nl/cutplanes.zip °  Molecular dynamics °  The YAMBER force field, ICMSB 2003 Figure: A snapshot from the movie Written by: Elmar Krieger License: GNU GPL Last modified: 2012/04/01 Download: http://yasara6.cmbi.ru.nl/yamber.zip °  Simulation and quantum mechanics of small molecules Figure: A snapshot from the movie This tutorial introduces fractional bond orders and pH dependency, shows how to build and simulate small molecules, and how to use quantum mechanics to optimize geometries and compare tautomers. Written by: Elmar Krieger License: GNU GPL, except coral reef background by Ove Hoegh-Guldberg (Centre for Marine Studies, University of Queensland) Last modified: 2012/04/01 Download: http://yasara6.cmbi.ru.nl/smallmol2.zip °  Accurate simulations in water Figure: A snapshot from the movie Written by: Elmar Krieger License: GNU GPL Last modified: 2012/04/01 Download: http://yasara6.cmbi.ru.nl/mdwater.zip °  The theory behind molecular dynamics simulations Figure: A snapshot from the movie Written by: Elmar Krieger License: GNU GPL Last modified: 2012/04/01 Download: http://yasara6.cmbi.ru.nl/mdintro.zip °  Interactive simulations for modeling Figure: A snapshot from the movie Written by: Elmar Krieger License: GNU GPL Last modified: 2012/04/01 Download: http://yasara6.cmbi.ru.nl/mdinteract.zip °  Molecular modeling °  Domain replacement Figure: A snapshot from the movie A tutorial explaining how to replace a loop or an entire domain, for example to create a hybrid template for homology modeling. Many thanks to Sven Geier for his 'Hidden' background (more at www.sgeier.net/fractals). Written by: Ahmet Sacan License: GNU GPL Last modified: 2012/08/26 Download: http://yasara6.cmbi.ru.nl/domainrep.zip °  Knowledge-based potentials Figure: A snapshot from the movie An overview of knowledge-based potentials. What they are, how to visualize them and how to use them. Written by: Elmar Krieger License: GNU GPL Last modified: 2012/06/03 Download: http://yasara6.cmbi.ru.nl/kbpotentials.zip °  Building small molecules Figure: A snapshot from the movie Written by: Elmar Krieger License: GNU GPL, except stellar nebula (copyright by Jaime Vives Piqueres) Last modified: 2012/04/01 Download: http://yasara6.cmbi.ru.nl/smallmol.zip °  Electrostatic potentials Figure: A snapshot from the movie A tutorial covering the different ways of representing electrostatic potentials using Particle Mesh Ewald and Poisson-Boltzmann methods Written by: Elmar Krieger License: GNU GPL Last modified: 2012/04/01 Download: http://yasara6.cmbi.ru.nl/electropot.zip °  Research topics °  PhD Thesis Defence 2004/09/27 by Elmar Krieger Figure: A snapshot from the movie Written by: Elmar Krieger License: GNU GPL Last modified: 2011/05/14 Download: http://yasara6.cmbi.ru.nl/thesis.zip °  CASP8 meeting on Sardinia 2008/12/04 Figure: A snapshot from the movie A summary of the protein structure prediction tricks used by YASARA during CASP8. Written by: Elmar Krieger License: GNU GPL Last modified: 2008/12/15 Download: http://yasara6.cmbi.ru.nl/casp8.zip °  Methionine Synthase Figure: A snapshot from the movie An overview of the catalytic activity of methionine synthase Written by: Richard Deth & Elmar Krieger License: GNU GPL Last modified: 2008/11/03 Download: http://yasara6.cmbi.ru.nl/metsynthase.zip °  PhD Thesis Defence 2006/02/09 by Sander Nabuurs Figure: A snapshot from the movie Written by: Sander Nabuurs License: GNU GPL Last modified: 2008/07/11 Download: http://yasara6.cmbi.ru.nl/thesis2.zip °  Multimedia °  Triple8 Celebration Figure: A snapshot from the movie A video game written in Yanaconda to celebrate the release of YASARA Structure and two anniversaries Written by: Elmar Krieger License: GNU GPL Last modified: 2012/04/01 Download: http://yasara6.cmbi.ru.nl/triple8.zip °  Buckynut Island Figure: A snapshot from the movie A video game written in Yanaconda to demonstrate the use of solids. Help Yami collect the Buckminster nuts. (Current highscore is 215 points by Bas Vroling) Written by: Elmar Krieger License: GNU GPL Last modified: 2012/04/01 Download: http://yasara6.cmbi.ru.nl/buckynut.zip °  The crazy pig animation Figure: A snapshot from the movie This is an example for multimedia animations, in honour of the Pink Pig (www.pinkpigpage.com). Written by: Emmanuel 'CrazyPig' Bettler License: Images copyright by pinkpigpage.com Last modified: 2009/05/02 Download: http://yasara6.cmbi.ru.nl/crazypig.zip °  The protein structure group at the CMBI Figure: A snapshot from the movie An introduction to the 'Vriend Group' at the CMBI, can be easily adapted to introduce your own research group Written by: Elmar Krieger License: GNU GPL, Grass texture by Rune S. Johansen Last modified: 2008/11/02 Download: http://yasara6.cmbi.ru.nl/cmbi.zip