Manual

In this module, you can select the bead file output options. Currently, we are providing three options, which can be independently activated (i.e., more than a single file type can be simultaneously written). These options are:

• SOMO. This is the new format developed for UltraScan-SOMO (default). In the first line are listed the number of beads (n) and then the partial specific volume vbar of the model. The properties of each bead are then listed in n successive lines of 8 columns each:
  x, y, z coordinates, radius, mass, color coding, correspondence with original PDB residue, bead ASA.
  At the end of the data, a descriptor of the content of the numeric fields (see above) is printed, followed by the list of the methods and parameters used to generate the bead model. This list will be displayed on the progress window of the main SOMO panel upon loading a SOMO-formatted bead model file.
• BEAMS. This is the originally developed old SOMO/BEAMS format. It is fully described in the original publications (Rai et al., Structure 13:723-734, 2005; Spotorno et al., Eur. J. Biophys. 25:373-384, 26:417, 1997). It basically consists of two files, one with the number of beads, vbar, and x, y, z coordinates, and the other with the radius, mass, color coding, and optional correspondence with original PDB residue (*.rmc file, see below).
• HYDRO. This is the format utilized by Josè Garcìa de la Torre's program Hydro. See here for more information.

In the Bead Sequence Format section, two mutually exclusive options are selectable, valid for all three formats:

• as in original PDB, which will list the beads in the same sequence as the original PDB residues from which they were derived (default).
  
• exposed side-chain-->exposed main-chain-->buried, which will list the beads according to the specified sequence.

The last option, which applies only to the old BEAMS format, allows to Include bead - original residue correspondence in the *.rmc file. This correspondance is always enclosed in the new SOMO format, and cannot be written in HYDRO formatted files.

This document is part of the UltraScan Software Documentation distribution.
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Last modified on March 1, 2010.