Ribbons Electron Density Example

To use the data preparation GUI type the following:

setup ribbons
ribbons-data prot (where "prot" is the name of your protein)

Fill in the name of your PDB file and click "Create prot.model"

Check "Enter Center" and "Center of enclosing box" and enter the coords of an atom you want the map to be centered on: i.e.

This should issue the following type of command:

pdb-model -t prot -e -o 13.42 45.33 27.20 prot.pdb prot.model

Then click "Setup prot.atoms". If you want to color by atoms click "Copy Default Color file" and then click "Edit Special Color file"; this will pop a vi session on "atoms.color". After this it should execute the following type of command:

pdb-sph atom -c atom.color -B prot.cyl prot.pdb prot.sph

Then click "Setup prot.polys"

Leave "Map" turned on, enter the name of the map file, the desired map contour level.

Click "Spherical Clipping" and enter the same coords as above and a Clip radius of 5.0

This should execute the following type of command:

facets -t 1.20 -k 8 -x 8.42 40.33 22.20 18.42 50.33 32.20 map.dn6 prot.tri

Click "ribbons -n prot &"

When you get the display, Click "Edit | Poly Control Panel | Draw Style=Lines"

Revised: Wednesday, 20-May-1998 15:06:08 EDT