MSROLL calculates molecular surface dots and associated unit normals of a protein molecule. The unit normals may be viewed on an SGI using the Inventor program ivview.
An example of the surface dots file for 4pti calculated by MSROLL is the following which is called prot.dot by the sample command:
atm r/c x y z A^2 cosx cosy cosz
1 0 0 1 26.614 26.886 -4.033 2.052 0.090 -0.343 -0.935
1 0 0 1 25.826 28.973 -2.446 2.052 -0.387 0.922 0.027
1 0 0 1 28.052 27.313 -2.921 2.052 0.962 -0.084 -0.261
1 0 0 1 27.514 28.560 -3.118 2.052 0.636 0.671 -0.381
1 0 0 1 27.711 28.277 -1.790 2.052 0.755 0.500 0.424
1 1 0 2 26.744 28.352 -1.114 0.669 0.313 0.637 0.705
1 1 0 2 25.821 28.820 -1.786 0.669 -0.250 0.922 0.294
1 1 0 2 27.239 28.008 -1.079 0.669 0.558 0.580 0.594
1 1 0 2 27.851 26.426 -2.520 0.669 0.845 -0.374 -0.381
1 1 0 2 27.989 27.288 -1.701 0.669 0.946 0.249 0.210
The normals image:
These results were obtained for 4pti by the following commands:
1. Get the PDB file
getentry 4pti
2. Extract the ATOM records:
extract pdb4pti.ent
3. Type the following command:
msroll -m pdb4pti.cln -p 1.4 -j prot.dot -o dots.iv
3. View the above results in prot.dot using your favorite editor or the normals using the following command:
ivview dots.iv
Last CSB Revision: Friday, 07-Feb-1997 16:43:00 EST