MSROLL calculates areas and volumes of a protein molecule by describing the molecule with solid geometric forms and then analytically computing the parameters. This method is in contrast to most other programs which use numerical methods.
An example of the areas and volumes summary for 4pti calculated by MSROLLis the following which is called prot.vol by the sample command file:
molecule name = 4pti
number of atoms = 454
probe radius = 1.400
contact area = 1256.921
reentrant area = 1927.293
molecular area = 3184.214
accessible area = 4009.115
solvent-excluded volume = 7113.969
component center volume molecular accessible
number x y z area area
1 15.204 21.291 4.195 7167.602 3107.523 4001.930
2 16.302 18.181 7.529 -53.632 76.690 7.185
In the above example component #1 is the outer molecular surface; component #2 is the cavity.
The individual atoms associated with each of the above surfaces may also be listed as in this example of a part of the area output file which is called prot.ara by the sample command file:
comp res # atm contact reentrant molecular accessible ... 1 ALA 58 N 1.583 7.294 8.877 5.410 1 ALA 58 CA 3.144 3.926 7.070 9.703 1 ALA 58 C 0.959 1.908 2.867 3.030 1 ALA 58 O 13.789 6.864 20.654 48.478 1 ALA 58 CB 24.721 8.441 33.161 72.960 1 ALA 58 OXT 10.459 8.508 18.967 36.769 2 GLU 7 OE2 0.000 3.403 3.404 0.001 2 PRO 8 O 0.116 7.168 7.284 0.409 2 TYR 10 N 0.350 6.205 6.555 1.195 2 TYR 10 O 0.153 6.267 6.420 0.537 2 TYR 10 CB 0.127 4.787 4.914 0.382 2 PHE 33 CZ 0.028 4.228 4.256 0.085 2 LYS 41 N 0.087 5.724 5.810 0.296 2 LYS 41 CB 0.530 10.494 11.024 1.599 ...
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 -v prot.vol -a prot.ara bca
3. View the above results in prot.vol and prot.ara
Last CSB Revision: Thursday, 30-Oct-1997 15:36:05 EST