An Introduction to Atom Selection

In this section it is assumed that you have the myoglobin structure mbco.pdb loaded and the views discussed in section 3.2 created. If this is not true, go back and repeat the process described there.

VMD has a powerful atom selection method which is very helpful when generating attractive, informative, and complex graphics. In the previous section you used a few of these atom selection tools. This tutorial assumes that you have already loaded the myoglobin molecule, but it isn't necessary to recreate all the graphical representations.

To change which atoms are used to display each representation of the molecule shown in the display window, open the Graphics window and select the representation you want to change. You can then either edit the different fields (selection, coloring method, or drawing method) or use the Delete button to delete the view entirely. Try changing or deleting some of the views. When finished, delete all representations for the myoglobin structure. To get the basic line drawing view back, clear the atom selection text entry area, enter all and press the Create Rep button.

Atoms may be selected on the basis of a property, i.e. protein or not protein, water, or nucleic backbone. They may also be selected by atom name, such as atom C, by residue name, such as resname HEM, or by many other identifiers. Multiple atoms may be specified with one keyword. For example, the selection name C CA N O will select the backbone atoms. (A similar effect may be obtained with the command protein backbone.) VMD can handle regular expressions, so that name "C.*" will select all atoms with names starting with C. VMD also understands the boolean operators and, or, and not, so the selection resname HEM and not name "N.*" selects all non-nitrogen atoms in the heme group of myoglobin.

Several more abstract selection criteria are available. For instance, the selection x $>$ 5 finds all atoms with an x coordinate greater than 5, while mass $>$ 12 and mass $<$ 14 selects all atoms with mass greater than 12 and less than 14 atomic mass units. Many math functions are also provided, so the selection sqrt( sqr(x) $+$ sqr(y) $+$ sqr(z) ) $<$ 10 will select atoms in a spherical region of radius 10 Å centered about the origin of the coordinate space. You can pick atoms nearby a selection with the phrase ``within $<$ distance$>$ of $<$ selection$>$ '' and all residues with the same property as a given selection as ``same $<$ property$>$ as $<$ selection$>$ ''.

See section 6.3 for a full description of the selection command.