Viewing the SURFNET surfaces

Viewing the maps in FRODO and O

If the (C)CP4 option is selected for the output file type, SURFNET will create density files in CCP4 format (extension .den). You can then use the CCP4 programs MAPPAGE or MAPMAN to convert the density files into brick maps suitable for display by FRODO or O.

As an example, the MAPMAN commands to convert a file called inhibitor.den might be

mapman

READ map1 inhibitor.den CCP4

MAPPAGE map1 inhibitor.map

quit

This will generate a brick map called inhibitor.map. To view in O, you need use absolute contour levels (rather than sigmas and RMS deviations). This is done by using two semi-colons in the map_param commands. For example,

map_obj map_i
map_file inhibitor.map
map_active_centre
map_param 50. 50. 50. 100.0 yellow ;;
map_draw

You may need to define the active centre of the map, and may need to make the extent of the map either smaller or larger than the 50x50x50 Å defined in the map_param command above.

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.