Options Add/Del help in adding/deleting cells when using batch selection (see Help | Keybindings).
VMD MEASURE RMSD UPDATE
They won't update while moving the mouse) but will change if you select/deselect a cell. Option keep allows you to fix Keys/Value.Look in men Help | Keybindings for other options to select/deselect cells.Their representation can be changed if you click in the tab Representations (this tab should be easy to understand) The color will change and the 2 structures (key1, key2) will be shown in VMD' graphic window. You will see the correspoding key and value (rmsd in this case) in the lower left. In the initial tab Graph you see a diagonal matrix, a color scale, a zoom interface, the calculation type options ( Set) and some matrix manipulation options ( Keys, keep.): In the new window you see 3 tabs (Graph, Representations, Info). It might take some time if you trajectory is large This will pre-align the pair of frames before calculating the rmsdĬlick on Calculate (upper center) and you will get a new window. Modifiers: Trace (behind the scenes this will transform the selection into "all and name CA")ī.Molecules: Top (your current top molecule in the main window 'T').Atom selection: enter all in the text field.Clculations on large trajectories might take a while, I recommend to use a small one while learning your way around the iTrajcompĬlick on tab Selection (upper right) and do your selection:
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