Your guide to YASARA View

°  Getting started °  The ten magic words °  Atom - YASARA's representation of a true atom °  Residue - any continuous stretch of atoms sharing the same residue name, residue number and molecule name °  Molecule - any continuous stretch of residues sharing the same molecule name °  Object - a collection of molecules and additional items °  Soup - all atoms in active objects °  Scene - all objects together °  All - the scene or the soup °  Bond - a covalent link between two atoms with pH dependent order °  Local coordinate system - The coordinate system within one object °  Global coordinate system - The coordinate system of the scene °  The three potential pitfalls °  You never get less than you want °  There is a difference between 'Hide', 'Switch off', 'Remove' and 'Delete' °  Gaps in a molecule are bridged by default °  The keys and mouse buttons to use °  Moving objects around °  Changing the scene style °  Editing °  Analyzing the soup °  Controlling a simulation °  Using the console °  Other keys °  The command line parameters °  Running YASARA in special environments °  Running YASARA without graphics °  Running YASARA on one machine with multiple users °  Running YASARA from an NFS mounted volume °  Running YASARA on a 64 bit operating system °  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 °  'Element' switches to a selection of chemical elements °  'SecStr' switches to a selection of secondary structure types °  'Segment' switches to a selection of macromolecular segments °  'AltLoc' switches to a selection of alternate conformations °  'Protein', 'NucAcid' and 'HetGroup' immediately select proteins, nucleic acids and the rest °  'Backbone', 'Sidechain' and 'Visible' immediately select backbone, side-chain and visible atoms °  'PDB', 'PDBRev', 'YASARA', 'IUPAC' and 'XPLOR' change the atom naming scheme °  'LocalX|Y|Z<>X' and 'GlobalX|Y|Z<>X' select atoms by their position °  'BFactor<>X', 'Occupancy<>X' and 'Property<>X' select atoms by B-factor, occupancy and property value °  'Charge<=>X' selects units by their charge °  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 °  The 'and', 'or' and 'not' operators perform logical operations °  The 'with distance <>X from' operator measures distances between atoms °  The 'with minimum distance from' operator finds the closest atom °  The 'with maximum distance from' operator finds the most distant atom °  The 'with <>X atoms closer Y among' operator counts close atoms °  The 'with <>X bonds to' operator analyzes bound atoms °  The 'with <>X bond angles to' operator analyzes second neighbor atoms °  The 'with distance <>X from Y surface...' operator measures distances from a surface °  The 'with contribution to X surface...' operator analyzes surface contributions °  The 'within sequence' operator selects within a given sequence °  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 °  New scene - Start again °  PDB files - Load and save objects in plain PDB format °  YASARA objects - Load and save complete objects °  YASARA scenes - Load and save the entire scene °  OpenBabel - Import and export molecules using OpenBabel °  Screenshots - Save plain or ray-traced screenshots °  MPEG movies - Encode plain or ray-traced animations °  Simulation snapshots - Load and save simulation states °  Exit - Quit YASARA °  Edit - Change content and properties of the soup °  History - Undo and redo changes °  Objects - Center, transform, transfer, remove, add and delete °  Split points - Edit split points, split and join entire objects °  Bonds - Add, type and delete bonds °  Building - Build atoms to molecules, oligomers, crystals and loops °  Geometry - Set or optimize distances, angles and dihedrals °  Sampling - Search conformational space °  Surface environments - Define the context of surface analysis °  Hydrogens - Add, swap and delete °  Water - Delete all waters °  Names and numbers - Set or get properties of atoms to objects °  Simulation - Simulate the soup °  Preparing a simulation - Define and fill the cell °  Force fields - Get the recipe °  Simulation parameters - Choose your favorite ingredients °  Restraints - Enforce distances and dihedral angles °  Running a simulation - Keep the soup from boiling °  Analyze - Analyze the soup °  Atom position - Calculate average positions and RMSFs °  Superposition - Align atoms and calculate RMSDs °  Contacts - List contacts and hydrogen bonds °  Energy - Calculate energies °  Electrostatics - Calculate electrostatic potentials and charges °  Geometry - Measure distances, angles, dihedrals and radii °  Rotamers - Show rotamer distributions °  Secondary structure - Calculate secondary structure content °  Surface areas - Calculate VdW, molecular and accessible surfaces °  Volumes - Calculate VdW, molecular and solvent accessible volumes °  Soup content - List, count and compare units, get boundaries °  Checks - Search for errors °  View - Change the appearance of the soup °  Colors - Add a fourth dimension to your figures °  Visibility - Show and hide, switch on and off °  Style - Display atoms as balls, balls&sticks, sticks and traces °  Secondary structure - Show tubes, ribbons and cartoons °  Surfaces - Show VdW, molecular and solvent accessible surfaces °  Hydrogen bonds - Show hydrogen bonds °  Atoms - Choose atom styles °  Projection - Switch the perspective °  Lighting - Light the scene °  Effects - Change and animate the scene °  Position - Place and move objects °  Orientation - Orient and rotate objects °  Labels - Display text labels °  Marks and zooms - Mark atoms with fireflies and zoom in °  Arrows - Show arrows connecting atoms or points °  Solids - Show spheres, boxes, pyramids, cylinders, tori and others °  Images - Show and animate bitmaps °  Text - Print text, possibly in 3D letters °  Options - Other commands °  Experiments - Let YASARA cook for you °  Macros - Watch YASARA do the work for you °  Tables - Collect, visualize and export data °  Formats - Choose the residue output format °  Logs - Redirect output to a file °  Plugins - Run plugins from a macro °  Default pH - Set the H+ ion concentration and residue pKas °  Quantum mechanics - Configure YAPAC °  Coordinate system - Live in a left or right handed world °  Units - Choose your favorite units °  Parallel computations - Configure multi CPU core usage °  Input devices - Configure the interaction with YASARA °  Shell - Execute shell commands °  Window - Change the display properties °  Location - Place the YASARA window °  Menus - Change the appearance of menus °  Console - Configure the console °  Antialiasing - Smooth is better °  Frequency - Change the frames per second and save battery power °  Stereo - Time to touch your molecules °  Help - Access the documentation and solve problems °  Manual - Browse the HTML documentation °  Installation - Download missing programs °  Index - All commands in alphabetic order

°  Run molecular dynamics simulations °  Preparing the topology °  Preparing the force field °  Running a simulation °  Analyzing a trajectory °  Playing back a trajectory °  Refine a homology model °  The quick method: in vacuo energy minimization with the NOVA force field °  The slow method: explicit solvent molecular dynamics simulation with the YAMBER force field °  Solve an NMR structure °  Setting the parameters °  Folding the structure °  Refining the structure in vacuo °  Refining the structure in explicit solvent °  Analyzing the ensemble °  Handling special cases like Cys-bridges, oligomers and metalloproteins °  Avoiding problems with hydrogen nomenclature °  Making floating assignments °  Create your own YASARA Movies °  Movies are written in Yanaconda °  Movies are stored in the yasara/mov directory °  Movies start with typical commands °  Movies can wait for a specified time or until you press a button °  Labels allow to jump back and forth between movie sections °  Work with YASARA and your text editor in parallel °  Movies can be imported from OpenOffice or PowerPoint °  Bitmap images can be displayed and animated °  Text can be displayed using 3D letters °  The look of the movie depends on the aspect ratio of the YASARA window °  Hints for using movies in important presentations

°  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 °  Integers remember the number of leading zeroes °  Floats remember their precision °  Weak strings are enclosed by single quotes °  Strong strings are enclosed by double quotes °  The left operand defines the datatype of the result °  Yanaconda supports the usual operators °  The negation operator has the maximum priority 7: !, not °  Operators with priority 6: *, /, //, %, <<, >> °  Operators with priority 5: +, - °  Operators with priority 4: &, |, ^ °  Operators with priority 3: >, >=, <=, <, ==, != °  Operators with priority 2: in °  Operators with minimum priority 1: and, or °  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 °  Loops can run over a range of numbers: for i = X to Y step Z °  Loops can run over a list: for i in X,Y,Z,.. °  Loops can run while an expression is true: while X and do .. while X °  Stop a loop with 'break' °  Loop ahead with 'continue' °  Lists are emulated with explicit evaluators °  Matrices are two dimensional lists °  The 'count' function determines the length of lists °  The 'min', 'max', 'sum', 'mean', 'stddev' and 'join' functions return the smallest, largest, sum, mean, standard deviation and concatenation of all list elements °  Lists can be sorted °  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 °  The header identifies a plugin °  The menu structure is enclosed in a triple-quote comment °  The layout for the remaining plugin differs between Python and Yanaconda °  Plugins can access most YASARA functions °  Python plugins can access a number of predefined variables °  Object descriptors identify selected objects °  Molecule descriptors identify selected molecules °  Residue descriptors identify selected residues °  Atom descriptors identify selected atoms °  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 °  The message './install_yasara: No such file or directory' appears in the Linux terminal °  YASARA does not start °  YASARA does not start from CD °  You are using Windows and nothing happens when you start YASARA °  A message about /dev/nvidiactl permission problems appears in the Linux terminal °  'Killed' or 'Segmentation fault' appears in the Linux terminal °  'Error while loading shared libraries' appears in the Linux terminal °  A red box appears: Error 2 - Essential videomode not supported under Linux °  A red box appears: Error 53 or 353 - No vector registers available or wrong CPU architecture °  A red box appears: Error 93 - Center of YASARA window off screen °  The YASARA windows stays empty and black in Linux °  YASARA displays an error-like message in the terminal °  The message '*** Assertion failure in -[NSEvent deviceDeltaX]' appears in the terminal °  The message 'Disabled smooth atom colors' appears in the terminal °  The message 'disabling TCL support' appears in the terminal °  The message 'libgcc_s.so.1 must be installed for pthread_cancel to work' appears in the terminal °  The message 'libGL warning: 3D driver claims to not support visual 0x4b' appears in the terminal °  The message 'Mesa X.Y.Z implementation error' appears in the terminal °  The message 'XFree86-DRI missing' appears in the terminal °  YASARA gets stuck in the startup screen °  YASARA displays a warning at the bottom of the startup screen °  Warning - Python not found °  Warning - Screen update not synchronized °  YASARA crashes right after the startup screen °  Something is wrong with the user interface °  YASARA crashes completely when you activate a menu °  It takes too long till the menu appears °  When the menu appears, the colors turn crazy °  Some menu entries are missing °  The mouse pointer disappears or flickers °  Some keys do not work as expected °  The Spaceball 3D controller does not work as expected °  YASARA runs slowly or displays incorrect graphics °  You have an unknown graphics cards, it is relatively old or has less than 16MB video memory °  You are running Windows Vista °  You are running Windows with an nVIDIA card °  You are running Windows with an ATI Radeon card °  You are running Linux with an nVIDIA card °  You are running Linux with an ATI Radeon card °  You are running Linux with a Xig graphics driver °  You are using a notebook °  You have an Intel 82845G graphics chip °  You have an Intel 82865G graphics chip °  You have an Intel 82915G graphics chip °  You have an S3 graphics chip °  You have a SiS M650 graphics chip °  You have a 3DLabs Wildcat card °  YASARA shows strange CPU usage patterns or crashes on dual core CPUs or dual CPU systems °  Something is wrong with your molecule °  You used OpenBabel ('other Fileformat') to read/write the 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 hangs, but other programs are not affected °  The computer freezes when you minimize the YASARA window °  The computer freezes when you start YASARA a second time °  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