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Cleaning electron density maps

  OBJECTIVE: This tutorial demonstrates how to read and display electron density maps, as well as how to use pseudo-density maps to clean up a map for presentation.

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 tex2html_wrap_inline6800 Density maps tex2html_wrap_inline6800 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 tex2html_wrap_inline6800 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 Emap_picked_atom macro 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 was written.)

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 tex2html_wrap_inline6800 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 tex2html_wrap_inline6800 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.

next up gif contents index
Next: Finding internal cavities in Up: Tutorials Previous: Electrostatics calculations

Jon Christopher
Tue Sep 14 16:44:48 CDT 1999