May 20 2013
Operations which use the ICM Biased Probability Monte Carlo method e.g. docking and loop modeling generate a stack of energy conformations.
MolMechanics/Stack/View will display the conformations of a stack in a table ranked by energy. Each conformation can be viewed by double clicking on the table. A stack file will have the extension .cnf. For example, after running the sample loop algorithm a stack of different loop conformations will be generated.
MolMechanics/Stack/Play This option will play the elements of the stack as a movie. You can set the number of frames for the movie and also select whether you would like ICM to interpolate between each frame. You can save this movie in avi, mpeg format using the Screen-Grabbing Movie options.
MolMechanics/Stack/Add current conformation This option will add the currently displayed conformation to the stack. This is useful for experiments such as multiple receptor docking whereby you dock to a stack of conformations.
MolMechanics/Stack/Store Stack in Object This option takes the current stack and stores it in a compressed form inside the specified object. The compressed stack can then be extracted with the load stack object command. Option stack of the montecarlo command stores the generated stack inside the current object automatically.
To view the stack in gui:
MolMechanics/Stack/Delete Deletes the current stack.
MolMechanics/Stack/Set conf Comparison This option compares the stack as described here: http://www.molsoft.com/man/preference.html#compareMethod and http://www.molsoft.com/man/icm-commands.html#compare
MolMechanics/Stack/Recalculate Energies Recaluclates the energy of a current stack if changes have been made.
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