wiki:BeadModelFileFormat

Field contents:

  • Line 1: Number of beads, Global partial specific volume
  • From line 2 on: X, Y, Z coordinates, Radius, Mass, Color coding, Correspondence with original residues, ASA
  • last line should contain the scale

Example:

10      0.788
1.0     0.0     0.0     0.5     400     2       test.1.2.3      3.1
2.0     0.0     0.0     0.5     400     2       test.1.2.3      3.1
3.0     0.0     0.0     0.5     400     2       test.1.2.3      3.1
4.0     0.0     0.0     0.5     400     2       test.1.2.3      3.1
5.0     0.0     0.0     0.5     400     2       test.1.2.3      3.1
6.0     0.0     0.0     0.5     400     2       test.1.2.3      3.1
7.0     0.0     0.0     0.5     400     2       test.1.2.3      3.1
8.0     0.0     0.0     0.5     400     2       test.1.2.3      3.1
9.0     0.0     0.0     0.5     400     2       test.1.2.3      3.1
10.0    0.0     0.0     0.5     400     2       test.1.2.3      3.1

Model scale (10^-x m) (10 = Angstrom, 9 = nanometer), where x is : 9

This bead model shows 10 touching beads in a straight line from left to right as seen in RASMOL, colored in green (color 2). The radius of each bead is 5 angstroms, and the molecular weight is 400 g/M for each bead, and the accessible surface area is 3.1 square nanometers for each bead. The bead model reference is a mock placeholder without meaning, and the model scale is in nanometers (9).

Rasmol visualization:

  • the x-axis goes from left to right, the y-axis goes up and down, and the z-axis goes in and out of the field of view.
  • the center of the molecule is automatically centered in the center of the field of view.

ASA calculations

  • there is no need for performing an ASA calculation since this is done twice, first, when converting a PDB structure to a bead model, then again when the bead model hydrodynamics are calculated.

Bead placement

  • it is important that beads are placed such that there is no overlap between beads. Beads can touch, though.
Last modified 5 years ago Last modified on May 12, 2013 11:38:32 AM