P I S A
Protein Interfaces, Surfaces and Assemblies
Contents • Start and run • Configuration File

Configuration File is essential for running PISA in command-prompt (non-graphical) mode, and may be also used for the configuration of QtPISA. QtPISA may be configured by either loading the configuration file in the Configuration Settings dialog, or by running the following command in terminal: 

qtpisa /path/to/pisa.cfg
where pisa.cfg is the configuration file with mandatory extension *.cfg. The above configuration command does not launch PISA for calculations, and only rewrites configuration parameters into local user's settings.

Configuration File is a plain-text file with simple keyword-parameter syntax:

For convenience, template Configuration File may be obtained from either PISA or QtPISA using one of the following commands: 
qtpisa -cfg-template > pisa.cfg
pisa   -cfg-template > pisa.cfg
Below is a sample of Configuration File, obtained in such way, which is produced with all explanatory remarks: 
# ------------------------------------------------------------------- #
#                                                                     #
#          This is configuratrion file for PISA software.             #
#                                                                     #
#   When used in command-prompt mode, this file must be specified     #
#       as last argument in thecommand line, or pointed out by        #
#              PISA_CONF_FILE environmental variable.                 #
#                                                                     #
#    This file may be also used to configure the QtPISA graphical     #
#   application, by either reading it using the "Load CFG" button     #
#  in PISA Settings Dialog, or by running QtPISA from command prompt  #
#    with this file as the only command-line argument. QtPISA needs   #
#           to be configure only once after installation.             #
#                                                                     #
# ------------------------------------------------------------------- #


#  DATA_ROOT must point on the directory to contain session
#  directories.
DATA_ROOT
/tmp/Eugene/


#  SRS_DIR must point on the directory containing SRS files.
SRS_DIR
/Applications/ccp4-6.4.0/share/ccp4srs/


#  MOLREF_DIR must point on the directory containing MolRef files.
MOLREF_DIR
/Applications/ccp4-6.4.0/share/pisa/


#  PISTORE_DIR must point on the directory containing files:
#          agents.dat
#          asm_params.dat
#          intfstats.dat
#          syminfo_pisa.lib and
#          rcsb_symops.dat
PISTORE_DIR
/Applications/ccp4-6.4.0/share/pisa/


#  HELP_DIR must point on the directory containing HTML-formatted
#  help files.
HELP_DIR
/Applications/ccp4-6.4.0/html/pisa


#  RASMOL_COM must give the rasmol launch command line
RASMOL_COM
/sw/bin/rasmol


#  JMOL_COM must give path to jmol.jar
JMOL_COM
/sw/Jmol/Jmol.jar


#  CCP4MG_COM must give the ccp4mg launch command line
CCP4MG_COM
/Applications/QtMG.app


#  SESSION_PREFIX is prefix for the names of session directories
#  created in DATA_PATH ("pisrv_" is used by default). Be sure to
#  have unique prefixes for each configuration file that is invoked
#  from a different user login or apache service. Session directories
#  are regularly removed from DATA_PATH, and SESSION_PREFIX allows
#  one to avoid permission conflicts between different services.
SESSION_PREFIX
__tmp_pisa_