next up gif contents index
Next: Locating a binding pocket Up: Tutorials Previous: Finding internal cavities in

 

Graphical surface selection

  OBJECTIVE: This tutorial demonstrates how to use graphical surface selection to create surface subsets.

Concepts introduced: Graphical surface selection (§ 6.11.3).

Start spock and type

fetch=12ca.pdb

to load the the structure of carbonic anhydrase. Type

makesurf

to build a molecular surface and accept the default value of 65 for the grid resolution. Now tear off the ``Graphics tex2html_wrap_inline6800 Mouse bindings'' menu to allow easier access to the graphical surface selection controls. We'll now look at the ``marking'' function. Select ``Mark surface'' from the Mouse bindings menu, and then select ``Clear filled surface''. Next, type

vc=d

to restore the default color for the surface. Press and hold the middle mouse button on the main surface, and trace out a roughly circular region, leaving a hole in the middle. You may wish to rotate the surface in order to make sure that the marked region is complete. Finally, choose ``Fill surface'' in the menu and click the middle mouse button in the interior of the marked region. If you've made a region without any holes, the fill command should fill only the interior of the region. If there are holes the entire surface will get selected, which means you'll have to clear the filled area, fix the holes and try again. You can also use the ``Fill slowly'' option to slow down the filling process. For either the fast or slow fill, you can interrupt a fill by pressing any mouse button. When you've completed a filled area, it can be referred to via the vsub=filled selection string. For instance,

vc=0,vsub<>filled

will hide all of the surface but the filled region. Similarly, the marked surface subset refers to the blue markings you've created. Use the Subsets tex2html_wrap_inline6800 Define surface subset to save the marked or filled region under another name. For example, we can call this region1, so enter region1 as the subset name, and vsub=filled as the selection string. Now click Z-Rotation/magnification in the mouse binding menu to turn off the marking functions. Finally, enter

vc=0;vc=d,vsub=region1

and only the region you've selected will be colored. You can use the newly created surface subset in any vertex selection string, including distance calculations (which you might use to find atoms close to a surface region). Obviously, in general use you'd want to make the marks around an active site or other area of interest instead of just any old surface region.


next up gif contents index
Next: Locating a binding pocket Up: Tutorials Previous: Finding internal cavities in

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