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MASS Web Server:

The web server runs MASS algorithm with the default values. It is recommended to use this option if you are not familier with the default parameters. If you wish to obtain more advanced alignments, you can download the software and play around with the parameters.
 
Field Description:

Ouput Description:

The mail that will be sent to the given email address will contain a zip file. After unzipping the attached file, a folder whose prefix is "mass" will be created. Under this folder there will be a file named "mass.output". 
This file will outline all the possible alignments found by MASS (the format of the file is explanined in the README file). The mass folder will also contain several sub-folders. Each sub-folder will describe a possible alignment and will contain the following files:

Running 
MASS:

Input:
The input for the algorithm is a set of m proteins: {P1, P2,...,Pm}. For each protein there are two inputs: One is the sequence of the 3D coordinates of its atoms in PDB format. The other is the assignment of SSE types to each residue in one of the following formats: PDB, DSSP and DSSPC.

Command line:

mass <PDB file> <PDB file> [options]
or
mass -f  <PDB list file> [options]

Where:

- <PDB list file> is a file listing the paths to all PDB files one wish to align. Listing the paths of all the PDB files in one file is a more convenient way when experimenting with many molecules and rerunning mass.

- options are:

  -c, --config=configuration file     configuration file. If not specified, the default parameters are used.

  -o, --output=output file              output file. If not specified, the output will be printed into a file named mass.output


For more details, please see the README file.