Options - Other commands

Some things are non-trivial. Nevertheless, YASARA delivers the answer at the touch of the 'Experiment' button. During an experiment, YASARA takes over control and uses its 'artificial intelligence' to do various things in the right order. A message at the bottom will keep you informed. Some experiments accept additional parameters, look at the example macros to see how it works.

Save YASARA's current state in a macro or record your input as a macro (excluding mouse movements), play back your own macros or those made by others with a higher stage of YASARA, stopping whenever you want. You can use the back/forward icons in the top right corner to jump around in the macro. Macros can wait for certain events before they continue, raise errors if something goes wrong, take a certain action if an error occurs, disallow user input, speedup animations if the graphics get slow , require a minimum YASARA version, and be applied to a certain target. You can save a lot of time by running macros in text console mode (start YASARA with command line parameter -con).

Many commands output a list of residues. Change the format for residue names if you log this output.

Many YASARA commands, especially those in the Analyze section, write their output to the console. You can log all output or just the result of the next command to a file and stop logging at a later point.

Normally plugins are run by clicking on the options they add to the menus. In some rare cases, it may help to create a plugin input file and then run a plugin directly. If there is a bug in the plugin and it crashes, you must additionally stop it before it can be run again.

YASARA normally assigns bond orders and protonation patterns according to pH 7.0. Here you can change this value and also assign pKas to certain residues, overriding YASARA's predictions made during the neutralization experiment.

YASARA provides semi-empirical quantum chemistry based on YAPAC, a derivative of James Stewart's MOPAC. Choose one of the MNDO, AM1 or PM3 methods, optimize geometries (possibly in water) and calculate formation energies .

YASARA's default is a left-handed coordinate system, feel free to live in a right-handed world .

By default, YASARA displays energies in kJ/mol. Here you can switch to kcal/mol .

Today's CPUs contain more than one core to speed up calculations. Here you can change the number of CPUs YASARA should use.

Choose between three different pointer styles , change the function of the mouse wheel , activate the P5 data glove or configure the Spaceball and its buttons .

Change or print your current working directory, delete files, get their size or run any other shell command.

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