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:
- PDB IDs separated by a space:
A list of at least two
PDB codes. Each code is a four character PDB ID, followed by a colon and
a list of chain IDs, e.g. 2pka:AB 3est 4cha:A 1ton 2ptn 3rp2:A.
- Your email address: MASS alignments will be sent to this
email address.
- Number of alignments:
The maximal number of alignments that
will be sent to the given email address.
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:
- A PDB file named 'fullAlignment.pdb': When loading this file
into a viewer, the alignened molecules will be shown completely.
- A PDB file named 'referenceAlignment': When loading this file
into a viewer, the reference molecule will be shown completely. For the rest
of the molecules, only their core, superimposed on the reference molecule,
will be displayed.
- A PDB file named 'coreAlignment': When loading this file into
a viewer, only the core of the alignment will be shown.
- A Rasmol script, named "script_fullAlignment.rsm". This script
loads the 'full_alignment.pdb file' and defines the core of the alignment.
To use this script execute: <your rasmol command> -script
full_alignment.pdb. Then, in the prompt of the Rasmol viewer, you
can select the core of the alignment ('select core') and manipulates it.
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.
