Volume and Area Calculation

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 
(which creates a file called pdb4pti.cln containing only ATOM records)

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