Index:
In order to make it possible to transfer data from one version of the Pronto program to another, two programs have been added to the Pronto program directory.
The export program exports the contents of a database into an ASCII file.
The import program imports the contents of the ASCII file into a database. This database could be an empty one, previously created by starting Pronto with the parameter EMPTY. The insertion of the default amino acids when Pronto is started with the parameter NEW is actually done by calling the import program after having inserted an empty database in the Pronto work directory.
You should be very careful if you try to modify text file produced by the export program, as little check for the integrity of the database structure exists during the import operation.
The programs are located in the directory:
$PRONTO_DIR/$PRONTO_VER/prog
The name inserted for $PRONTO_VER should match the date of the database.
The names of the programs depend upon the machine on which you are working:
Machine: Name of export program: Name of import program:
SGI COFF expIO impIO
SGI ELF expIO4 impIO4
IBM RS/6000 expIBMO impIBMO
SUN SPARC expSO impSO
SUN Solaris expLO impLO
Linux expQO impQO
The export program is started within the directory in the PRONTO_DATA directory containing the database to be exported. The export program does not modify the database files themselves, but creates files with the extension: ".dump".
To import the files, create an empty database by starting Pronto with the parameter EMPTY. Exit Pronto, and store the database under a new name. Move the *.dump files to the directory containing the empty database, and import the ASCII files by starting the import program with the parameter: *.dump
To make some of the operations mentioned previously easier to perform, some script files have been made to do some simple operations.
Note: The term: "3D database" simply means a database created with the 3D version of Pronto. It does not have to contain information from 3D spectra.
The most common use of the export/import programs is, if you receive an update of the Pronto program and this new version is using a new database layout. After having installed the new version and modified the date for the PRONTO_VER variable in the .cshrc file, simply convert an old database by giving the command:
ConvertDB <old date> <name of database> [NOKEEP]
The <old date> should be a six-digit number. This is used to locate the old version of the export program. It is thus important not to delete an old version of Pronto until you have converted all your databases. You can reinstall an old version of the Pronto program for purpose of converting a database in its format without having a valid license for that version, i.e. if it has expired. The NOKEEP option means that the convertion should use the atom name table that is contained in the EmptyDB directory instead of the one contained in the old database.
You can also convert a Pronto database into the same version. This is useful to reclaim space in the database from deleted entries.
This script file is used to convert a database created with the old, 2D version of the Pronto program into a format readable by the new version of the program. Note: It is not possible to convert a 3D database back to a format readable by the 2D version of Pronto.
The conversion requires five operations, and can take quite a while to perform.
The conversion is easiest to perform if the 3D version of Pronto uses the same path for the PRONTO_DATA environment variable as the 2D version did, else you would have to move the database files manually from the 2D directory to the 3D directory.
The actual conversion is done simply by giving the command:
convO <database name>
The script file will print out some information about where to locate the old database, if something goes wrong.
To optimize speed, Pronto databases are stored in binary format. This makes it impossible to use a database created on e.g. an SGI machine on a Linux machine.
To convert an SGI database to Linux format you'll need access to both an SGI machine and a Linux machine. Follow the instructions below:
On the SGI machine:
cd $PRONTO_DATA/olddata $PRONTO_DIR/$PRONTO_VER/prog/expIO4
On the Linux machine:
Pronto EMPTY
Immediately exit Pronto, and store the empty database under a name, e.g. newdata.
Still on the Linux machine:
cd $PRONTO_DATA/newdata cp ../olddata/at_index.setup . cp ../olddata/pronto_win.ini . $PRONTO_DIR/$PRONTO_VER/prog/impQO ../olddata/*.dump
Now you can start Pronto newdata on the Linux machine!
You can use this recipe to convert between any architecture. It is also possible to convert from an old version of Pronto, replace $PRONTO_VER as needed.