Viewing the SURFNET surfaces

Viewing the maps in SYBYL

The contour files generated for SYBYL will have a .cnt extension. Before reading the maps into SYBYL, check the Surface Style setting. For small maps you can use the Opaque option which shows the contours as solid, rendered surfaces. For larger surfaces, this type of surface can take a long time to generate and be slow to move around the screen. So, for large surfaces (eg the surface of the whole protein), set the surface style to Standard, which gives chicken-wire representations of the contour surfaces.

To read in a contour map enter the following commands:-

Sybyl> CONTOUR
Sybyl> DISPLAY
Sybyl> D1 or D2, D3 or D4.
Sybyl> 100.0
Sybyl> GREEN or any other colour

Use a single contour level of 100.0 for van der Waals surfaces and gap regions. For density distributions, use whichever contour level is most appropriate.