Concepts introduced: reading XPLOR files (§6.1.1), Contouring electron density and creating density masks (§ 6.4.7), math operations on maps (§ 6.6.2).
Note: this tutorial requires you to have an XPLOR-format electron density map and a corresponding PDB file. If you don't have an XPLOR map, you should create a pseudo density map by reading a PDB file, and then using ``Alter Density maps Make pseudo density map''. Realize that this is just a cheap imitation of the real thing.
Begin by starting spock and reading your PDB file. You can then read in your XPLOR file with the
command or by using the menu system. Spock should print a summary message once the read is complete. First turn on density map display in the ``Display'' menu. To contour the density map, use the ``Alter Density maps'' menu, and select the option ``Density contour 1''. You'll be presented with a dialog box which asks 1) which map to contour, 2) the contour level, 3) the color to use for the contour, 4) which atoms on which to center, 5,6 and 7) the X, Y and Z coordinates of the center, and 8) the length of the cube which will encompass the contoured region.
We want to contour map 1 at level 1.0 with the color blue (4). The center atoms prompt and X/Y/Z prompts are two ways of specifying the center of the contouring region. If the center on atoms string is not ``None'', then the map is constructed centered on the specified atoms. If the string is ``None'', then the X, Y, and Z coordinates are used. These XYZ coordinates are usually the coordinates of the last picked atom, making it easy to center your contours on a given region. For the tutorial, let's change things slightly, and specify that we want to be centered on the first atom, so enter
(or some other atom that you think is on the surface of your
protein) in the center on atoms box. Press enter, and you should electron
density map contour.
We can use a variation of the ``look'' shortcut described in the first
tutorial (§8.1) to good effect for electron density maps,
and set up a method to automatically contour around a picked atom. Under
the ``Picking'' menu, choose ``Command'' and enter
mac=Emap_picked_atom;look=10 into the resulting dialog. Now,
whenever you pick on any object, the first density contour will be rebuilt
centered on that atom, and any bonds within 10 Ångstroms of that
position will be drawn. As written, the
only contours map 1, at 1.0 sigma, but you can create your own version of
the macro if you wish. (Look at $SPOCK/Spockrc to see how the macro
If your map is like most maps, there will be a fair amount of extraneous density outside the protein, for which there are no associated atoms. If you wish to clean this density up for clarity of presentation, you may create a density mask. Choose ``Make positive mask'' from the ``Alter Density maps'' menu. Accept 0.0 as the cutoff. Now a positive mask of the same dimensions as the original map has been created (as emap2) with 1.0 where there are atoms and 0.0 where there are not. If we multiply this map by the original map on a point-by-point basis, regions where there are no atoms will have a 0 density. To do this multiplication, choose the ``Calculate Properties math'' menu, and select the ``Multiply two properties'' option. Choose ``emap 1'' and ``emap 2'' from the next two menus, and choose ``emap 2'' as the location to store the result. Finally, go back and contour emap 2 as Density contour 2 the same way you contoured emap 1, making sure to specify map 2 in the dialog box. Emap 2 should be a cleaner version of the map, with density only where there are atoms. You may wish to turn off Density map 1 so that you can more clearly see the results.