Features

After downloading the project, install it and set the environment variables (as described in Victor page). You can then use the command:

PdbSuperimposition

Running the program without any parameters or with the option -h will show the description and the indications of how to use it.

The output is:

Pdb Superimposition -- calculate the superimposition scores (RMSD/MaxSub/GDT_TS/TM) of two pdb files
Options: 
	-i <filename> <filename>, 	 Input PDB filename
	[-r], 	 Calculate only RMSD score
	[-m], 	 Calculate only MaxSub score
	[-g], 	 Calculate only GDT_TS score
	[-t], 	 Calculate only TM score
	[-L <seed>], is a integer number for the initial seeds lenght of MaxSub
	 	used by MaxSub, GDT_TS, TM-Score (default is 4)
	[-d <threshold>], is a double number for the threshold of MaxSub (default is 3.5A)
Usage: 
	PdbSuperimposition -i <file_name> <file_name> [-<char_score>] [-L <integer_seed>] [-d <double_threshold>]

##Required parameter

• -i: only this parameter is required, the others are optional. The parameter -i is necessary for the two input pdb files for evalutate the optimal structural superimposition. Example:

    Superimposition -i file1.pdb file2.pdb
  

The output consists of a view of all scores on the terminal, together with the generated pdb files for the superimposition, located in the directory the program was run.

##Optional parameters

• [-L <seed>]: it is possible to choose with an integer number the length of the initial seeds for the MaxSub algorithm. If the parameter is omitted the default number is 4;
• [-d <threshold>]: it is possible to choose with a double number the maximum distance (in Angstrom) for the copple of atoms for the MaxSub algorithm. If the parameter is omitted the default number is 3.5;
• [-r]
• [-m]
• [-g]
• [-t]

With the last four parameters it is possible to calculate one or more available scores, excluding others.