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Advanced Mouse Controls

Picking Atoms and Bonds

The current mouse confiruation is visible on the lower right-hand corner of the screen as a matrix. Under the default mouse configuration:

Whenever an atom or bond has been picked, a number of atom selections are automatically defined as described in the following table:

You can click on a selection name to see visually which atoms are included in the selection. All of these selections can be used and manipulated as if they were created manually using the select command. Note however, that these selections are quite fragile, and will be automatically deleted in response to a number of common occurences, such as loading a new object.

Example Usage of the "pk" Atom Selections

Assuming that you picked an atom or bond...

   show sticks,(pkresi)     # show sticks on the residue you picked

   color read,(pkchain)      # color the chain you picked

   remove (byres pk1)        # removes all atoms in the residue you picked 

The "lb" and "rb" Selections

Most of the time, the "pk1" atom selection will suffice. However, there are times when you need to specify two or more sets of atom selections. This is where "lb" and "rb" come in.

In addition to the "pk" atom selection set, there are two more atom selections which can be manipulated with the mouse. These are: (1) the left-button or "lb" selection and (2) the right-button or "rb" selection. Under the default mouse configuration:

Certain commands are designed to use "(lb)" and "(rb)" as default arguments. For instance, the "distance" command, if called without any arguments, will attempt to create a distance object between the (lb) and (rb) selections if they exist

    # define (lb) by CTRL-SHIFT/left-clicking one atom
    # define (rb) by CTRL-SHIFT/right-clicking another
    dist  # will create a distance object between the two atoms.

Conformational Editing

Sorry, no documentation yet -- these features won't be too useful until PyMOL is coupled up with an energy minimiation engine.

NOTE: This manual is a PyMOL Incentive Product with a One-Year Evaluation Period. You, your school, or your employer must purchase a PyMOL License & Maintenance Subscription to cover usage beyond the first year. We trust you to support the PyMOL project via the "honor" system, so please do your part! See Usage Terms for more information.
Copyright © 2004 DeLano Scientific LLC. All Rights Reserved.

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