Your guide to YASARA View

°  Getting started °  The ten magic words °  The three potential pitfalls °  The keys and mouse buttons to use °  The command line parameters °  Running YASARA in special environments °  Working with extremely large protein structures °  Citing YASARA, its algorithms and force fields °  Reporting bugs, problems and inconveniences °  Screenshots as examples of what you can do

°  Selections are defined by a final type and an expression °  Possible final selection types are All, Obj, Mol, Res and Atom °  Ranges can be specified with a minus sign °  A logical OR is assumed between items of the same selection type °  A logical AND is assumed if you switch the selection type °  Selections are inflated to the final selection type at the end °  Additional selection types allow to filter for various properties °  Names can be negated with an exclamation mark '!' °  Names can be wildcards using a question mark '?' °  Names with unusual characters can be quoted °  Selections can be combined with explicit operators °  Selections are not case sensitive except for two special cases °  Selection windows allow to build selections with the mouse °  Yanaconda helps to define selection subsets °  Examples of selections needed in real-life

°  File - Load and save the scene or parts of it °  Edit - Change content and properties of the soup °  Simulation - Simulate the soup °  Analyze - Analyze the soup °  View - Change the appearance of the soup °  Effects - Change and animate the scene °  Options - Other commands °  Window - Change the display properties °  Help - Access the documentation and solve problems °  Index - All commands in alphabetic order

°  Run molecular dynamics simulations °  Refine a homology model °  Solve an NMR structure °  Create your own YASARA Movies

°  Macros can be recorded or written manually °  Yanaconda is Yet ANother Abridged COding 'N' Development Approach °  Yanaconda is a reinterpreted language °  Explicit evaluators modify the source code at run time °  When writing Yanaconda macros, use Python syntax highlighting °  The four datatypes are integer, float, weak string and strong string °  The left operand defines the datatype of the result °  Yanaconda supports the usual operators °  Indentation defines the program flow and must be a multiple of two spaces °  Control the program flow with if, elif and else °  There are four types of loops °  Lists are emulated with explicit evaluators °  Yanaconda macros can access predefined variables °  Yanaconda macros can include each other °  Calls to built in functions can be placed anywhere within an expression °  Calls to YASARA commands must appear one per line °  Macros can be speeded up by switching off the console

°  Plugins allow you to add your own menu options °  Plugins can be written in Yanaconda or Python °  Python can be downloaded from www.python.org °  Plugins must stick to format conventions °  Plugins can access most YASARA functions °  Python plugins can access a number of predefined variables °  Python plugins run in a separate thread °  Plugins can be speeded up by switching off the console °  Plugins can be run from the command line and in console mode °  Debugging is done by adding temporary print commands

°  Windows users can obtain Python from www.python.org °  Copy and import yasara/pym/yasara.py °  There is a Python function wrapper for most YASARA commands °  Python functions return either nothing, a single value or a list °  YASARA specific data is available in 'info' °  YASARA commands with multiple formats map to different Python functions °  A subset of the YASARA soup can be obtained as a pdb_file instance °  The console needs to be switched off for maximum performance °  There is a specific Python function for each experiment °  The Python module can run YASARA in graphics or text mode

°  Known inconveniences °  YASARA cannot be installed °  YASARA does not start °  YASARA displays an error-like message in the terminal °  YASARA gets stuck in the startup screen °  YASARA displays a warning at the bottom of the startup screen °  YASARA crashes right after the startup screen °  Something is wrong with the user interface °  YASARA runs slowly or displays incorrect graphics °  YASARA shows strange CPU usage patterns or crashes on dual core CPUs or dual CPU systems °  Something is wrong with your molecule °  YASARA does not behave as expected with two or more connected monitors °  Quad-buffered stereo cannot be activated or flickers. °  YASARA fails to run Python plugins or other programs like PovRay, OpenBabel, MSMS °  YASARA or the entire computer freezes °  YASARA quits with a red error box or crashes sometime later °  The Twinset encounters a technical problem °  Forwarding the YASARA window via SSH does not work