3. Visualize sequence conservation onto the 3D structure :

        How to map data to structure using GRASP

The GRASP property file consists of a list of values (one value for each atom on the PDB file).

Once you created your GRASP property file using Blast2Grasp, here are the GRASP commands to map your data to your structure. You can choose a Worm representation or you might prefer a Surface representation. In any case, you'll want to change the color settings.


Grasp worm

Worm representation

  • Read / PDB File
  • Read / GRASP Property File
  • Build / Backbone Worm / Carbon Alpha Worm
  • Display / Hide / Bonds
  • Calculate / Simple Property Math / Map Atom Value to Worm / All Atoms / General Property #1 / General Property #1


Grasp surface

Surface representation

  • Read / PDB File
  • Read / GRASP Property File
  • Build / Molecular Surface / All Atoms
  • Calculate / Simple Property Math / Map Atom Value to Surface / All Surfaces / All Atoms / General Property #1 / General Property #1
  • Display / Alter / Molecular Surface / General Property #1 / Lit and Rendered

Color settings

You can change your color settings by right-clicking on Worm Prop. 1 or Surface Prop. 1 near the color bar and selecting Input Color Values. You can also change the value range by selecting Input Relative Values.

You will find a nice color chart here to help you enter RGB values for your favorite colors.