PISA (CCP4: Supported Program)

NAME

pisa - Protein interfaces, surfaces and assemblies

USAGE

1. Perform PISA analysis of a structure given in PDB or mmCIF file 'coorfile':

    # ./pisa name -analyse coorfile [cfg]
    

   where 'name' is a mandatory session name, [cfg] stands for optional configuration file. Configuration file must be specified unless pointed out by environmental variable PISA_CONF_FILE. After finishing, the results will be stored in session directory identified by session name 'name'. Use the following commands for retrieving the results.

2. Retrieve lists of interfaces, monomers and assemblies:

    # ./pisa name -list {interfaces|monomers|assemblies} [cfg]
    

3. View an interface, monomer, assembly or a dissociate:

    # ./pisa name -view spec serial_no [cfg]
    

   where spec={interface|monomer|assembly|dissociate}, and serial_no is serial number shown in the corresponding list.

4. Download an interface, monomer, assembly or a dissociate:

    # ./pisa name -download spec serial_no [cfg] > output_file
    

5. Get details of an interface, monomer or assembly:

    # ./pisa name -detail spec serial_no [cfg]
    

6. Generate Remark 350:

    # ./pisa name -350 assembly_serial_no [cfg]
    

7. Generate XML output:

    # ./pisa name -xml [cfg] > outputfile.xml
    

8. Erase session data:

    # ./pisa name -erase [cfg]
    

DESCRIPTION

PISA is an interactive tool for the exploration of macromolecular (protein, DNA/RNA and ligand) interfaces, prediction of probable quaternary structures (assemblies), database searches of structurally similar interfaces and assemblies, as well as searches on various assembly and PDB entry parameters.

Reading the Ouput:

Problems:

AUTHOR

Eugene Krissinel and Kim Henrick, EBI

CITATION

E. Krissinel and K. Henrick (2005). 
Detection of Protein Assemblies in Crystals. In: M.R. Berthold et.al. (Eds.): CompLife 2005, LNBI 3695, pp. 163--174. Springer-Verlag Berlin Heidelberg.

The citation will change for the following

E. Krissinel and K. Henrick (2007). 
Inference of macromolecular assemblies from crystalline state. Journal of Molecular Biology, accepted for publication on 08.05.2007.

SEE ALSO