Manual

Here we describe the SOMO bead model format.

Bead model files produced in the SOMO format have the extension ".bead_model".

Following is an example from a small bead model containing three beads:

    3	0.676
    -12.3000	15.2190	16.4980	2.1710	16.030003	1	HIS.PB.A.15	70.7094
    -11.8771	15.7328	18.9793	2.5584	41.029999	1	HIS.PB.A.15	67.4832
    -9.5665	12.0546	16.9414	3.5728	80.103195	4	HIS.SC.A.15	203.3945
    
    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
    
    Bead Model Output:
      Sequence:                   as in original PDB file
    
    Model scale (10^-x m) (10 = Angstrom, 9 = nanometer), where x is : 10
    Bead model built with the following options:
    ASA Calculation:
      Perform ASA Calculation:    On
      ASA Method:                 Rolling Sphere
      ASA Probe Radius (A):       1.40
      SOMO ASA Threshold (A^2):   20.0
      SOMO Bead ASA Threshold %:  50.0
      ASAB1 Step Size (A):        1.0
    
    Miscellaneous options:
      Calculate vbar                 On
      pH                             14.00
      Enable Peptide Bond Rule       On
    
    Molecular weight total: 137.16 [Da]
  

• Line 1 contains the following fields:
  1. the Number of beads
  2. the partial specific volume
• Line 2 through the number of beads plus 1 (4 in this case) contain the bead definitions consisting of the following fields:
1. X coordinate
2. Y coordinate
3. Z coordinate
4. Radius
5. Mass
6. Color coding
7. Correspondence with the original residues
• For manually created bead models this can be any useful reference text
8. Accessible surface area
• If unknown, you can put 0
• Note that all fields described above can be separated by one or more spaces and/or tab characters.
• Lines starting at the number of beads plus 2 (5 in this case) and after are purely comment lines and can contain any text. However, line 13 is a special case which is recognized as the model scale for the bead model file. It can be specified on any line in the comment area. If not specified, a warning will be given upon loading the bead model file.

This document is part of the UltraScan Software Documentation distribution.
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The latest version of this document can always be found at:

http://somo.aucsolutions.com

Last modified on February 27, 2021.