Hi Natalie, If the inner surface is totally disconnected from the outer surface (like an inside "bubble"), it is fairly easy: - Ctrl-click to select the surface - use command: ac Sc (this makes the disconnected parts into separate "surface pieces" that can be controlled separately; choose "Favorites... Command Line" from the menu to get the command line) - Ctrl-click empty space to clear selection - Ctrl-click outer surface to select it (now the inner surface will not be selected) - choose "Actions... Inspect" from the menu to open the Selection Inspector. In that dialog, Inspect "Surface Piece" and set "displayed" to "false." That will undisplay the outer surface, leaving the inner surface. If there are other pieces to turn off, repeat by selecting them and using the Selection Inspector to undisplay them. If inner and outer surfaces are connected, however, it may be difficult to just show the part you want. You can select sets of atoms and use "Actions.... Surface... hide/show" to hide or show their surface patches, but the problem is that it can be hard to figure out which atoms go with which surface patches, and some atoms might even form parts of both the inner and outer surfaces. A third possibility is to use the Surface Zone tool (under Tools... Surface/Binding Analysis). In that case you would need to put some atom in the middle of the inner surface, select it, and then use some cutoff from that atom. You can add a single atom with Build Structure (under Tools... Structure Editing), Add Atoms section, "atom" (make sure to put atom in a "new model") and then move it relative to your first structure by checking/unchecking the boxes under the Command Line and using the mouse. It can be hard to get the atom where you want it, and even if that part is successful, it may work very well either if a spherical cutoff does not separate the inner and outer surfaces. The "Structure Analysis and Comparison" tutorial includes showing just the surface of a binding pocket: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ squalene.html#surfaces> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 22, 2009, at 2:07 AM, Xarana wrote:
Hi Elaine, Thank you very much for your quick help. That really helped a lot and the differences are small. One last question:
Is there a possibility to only show this "inner surface" without the outer one for more clarity? I have to compare in 10 different structures (NMR solved) the extent of this cavities. And sadly SYBYL is not able to save as any other file format.
Best wishes, Natalie Bordag PhD student