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To install a movie, just download the ZIP file and unpack it in the yasara/mov directory
(which of course requires that you have at least YASARA View installed).
MacOS tries to hide the yasara directory from you: open Finder, browse to the YASARA application
and click on 'Show package contents' in the context menu to see the yasara directory. If you then click on Help > Play help movie, the new movie will appear in the list. Movies are simply YASARA macros that use multimedia elements to create
interactive tutorials or presentations. Works well instead of the usual
PowerPoint approach. Instructions how to create your own movies can be found
in the YASARA documentation by clicking on 'Recipes - Answer complex questions' ->
'Create your own YASARA movies'.
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 | | Figure: A snapshot from the movie |
| A journey through YASARA's drug design functionality. Using an inhibitor for HIV protease as example, this help movie shows how to visualize protein-ligand interactions, predict ligand binding affinities and improve ligands with the small-molecule builder. Many thanks to Sven Geier for his 'Tetris' background (http://www.sgeier.net/fractals). Written by: Elmar Krieger License: GNU GPL Last modified: 2023/01/24 |
° | 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: 2020/05/18 |
 | | 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: 2020/05/16 |
° | 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: 2020/05/12 |
° | 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: 2020/05/09 |
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Plugins are Python scripts or Yanaconda macros that extend YASARA's user interface
and get activated when you click the respective option. They are the method of choice
to extend YASARA with your own functions. All plugins are distributed together with YASARA and should be available from
the graphical user interface. Windows users need to have Python from www.python.org
installed. To reinstall a plugin, just download the ZIP file and unpack it in the yasara/plg directory.
If you then restart YASARA, the new options will appear in the menus. If you are not
sure where the option appears, look at the top of the main plugin file (*.mcr or *.py).
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° | FoldX forcefield plugin |
This plugin provides access to various tools from the FoldX molecular modeling and design program in YASARA. FoldX can be obtained from http://foldx.crg.es. Plugin updates and documentation are provided at http://foldxsuite.crg.eu/products#yasarapg Especially for academics, commercial users need a FoldX license. Written by: Javier Delgado and Joost Van Durme License: - Last modified: 2025/09/17
This plugin provides access to the structural alignment software MMLigner Written by: James Collier, Alexander Botzki. VIB License: GPL3 (www.gnu.org) Last modified: 2024/09/03
This plugin performs a structural alignment with the help of various programs or web servers: Sheba by J.Jung & B.Lee, which is downloaded automatically from http://rex.nci.nih.gov/RESEARCH/basic/lmb/mms/sheba.htm in Linux, Multiprot by Shatsky, Nussinov & Wolfson and CE by Shindyalov & Bourne. YASARA Plugin developed at the IBCP France, see http://pbil.ibcp.fr/~ebettler/stages/mroche/. Click Analyze > Align. Written by: Mikael Roche & Emmanuel Bettler License: GNU GPL Last modified: 2024/07/30
° | Interactive oligosaccharide builder |
This plugin performs interactive building of oligosaccharides Written by: Elmar Krieger License: GNU GPL Last modified: 2017/09/20
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Macros are written using the Yanaconda language. If you already know a programming
language, you can learn Yanaconda in 15 minutes, otherwise it may take 30. To install, just save the macro in the directory yasara/mcr or wherever you want it.
The syntax of Yanaconda is described in the YASARA documentation.
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This macro provides a function library for assembling giant structures with millions to billions of atoms, to be 'included' by other macros Written by: Elmar Krieger & Kornel Ozvoldik License: GNU GPL Last modified: 2023/10/16
° | Running an energy minimization |
This macro runs an energy minimization of the soup without cleaning it first. Compared to the normal minimization experiment, it temporarily adds a water shell so that all force fields can be used directly, also those optimized for use with explicit solvent Written by: Elmar Krieger License: GNU GPL Last modified: 2019/11/22
° | Running an energy minimization |
This macro cleans the soup and then runs an energy minimization. Compared to the normal minimization experiment, it temporarily adds a water shell so that all force fields can be used directly, also those optimized for use with explicit solvent Written by: Elmar Krieger License: GNU GPL Last modified: 2019/07/06
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