VMD User's Guide

• -dihomo: Use a diatomic molecule probe with two identical (homogeneous) atoms, insteadof using a single atom as a probe.• -dihetero: Use a diatomic molecule probe with two different (heterogeneous) atoms, insteadof using a single atom as a probe.• -conf numconf: Sample a number numconf of different random rotamers of a diatomicmolecule at each grid point.• -probe1 epsilon Rmin/2: Set the CHARMM van der Waals/Lennard-Jones parameters forthe monoatomic probe, or for the first atom of a diatomic molecule. Units of epsilon arekcal/mol, and of Rmin/2 are Å.• -probe2 epsilon Rmin/2: Set the CHARMM van der Waals/Lennard-Jones parameters forthe second atom of a diatomic molecule.• -bond length: Set the bondlenth of a diatomic molecule. Units of Å.• -cutoff cutoff: Set the CHARMM van der Waals cutoff beyond which the interaction betweenthe probe and protein atoms is set to zero.8.3.35 waitSpecify a number of seconds to wait before reading another command. Animation continues duringthis time. The wait command will not behave as expected if called within a complex Tcl proc orloop structures. The wait command doesn’t actually run until the next complete Tcl code blockdue to the way VMD processes its commands.• time: waittime seconds.8.3.36 sleepSpecify a number of seconds to sleep before reading another command. Animation stops duringthis time.• time: sleep time seconds.8.4 Tcl callbacksWhen certain events occur, VMD notifies the Tcl interpreter by setting certain Tcl variables tonew values. You can use this feature to customize VMD, for instance, by causing new graphics toappear when the user picks an atom, or recalculating secondary structure on the fly.To make these new feature happen at the right time, you need to write a script that takes acertain set of arguments, and register this script with the variable you are interested. Registeringscripts is done with the built-in Tcl command trace;seehttp://www.tcl.tk/man/tcl8.4/TclCmd/trace.htmfor documentation on how to use this command. The idea is that after you register your callback,when VMD changes the value of the variable, your script will immediately be called with the newvalue of the variable as arguments. Table 8.4 summarizes the callback variables available in VMD.118