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

Like many other programs, on start-up, PISA performs a set of initialisations, which include reading and checking for consistency some 30Mb of various data. Therefore, a few-second delay is possible on slow systems.

If initialisation fails in any part, this is due to either corrupt data files or wrong configuration settings. Configuration settings are accessible through View/Settings menu item (qtpisa/Preferences on Mac OSX), or by clicking on the Settings button in the Toolbar, or pressing Ctrl-G (⌘-G on Mac OSX) hot key. Consult configuration pages for further details.

After successful initialisation is successful, QtPISA is ready for user's input, which is indicated by the welcome message in the working area of the window. The input may be:

  1. A coordinate file in PDB or mmCIF format. Select File/Open file menu item, or push the Open button in the Toolbar, or press Ctrl-O and navigate to the file in your file system, or drag-and-drop from your file manager (Windows Explorer (MS Windows), Nautilus (Linux), Finder (Mac OSX)). The file may be also specified as a command-line argument, when starting QtPISA in a termoinal window.
  2. QtPISA Result File *.pisa, containing results from previous calculations. The file is open in the same way as above.
  3. A PDB Entry Code. Select File/Open PDB online menu item, or push the Download button in the Toolbar, or press Ctrl-L, then set up PDB code in the pop-up dialog box, and press Download button in the dialog. The corresponding PDB file will be downloaded from the Protein Data Bank and used as if it were read from local file system.
Once an input is done, calculations start automatically. The calculation time may vary significantly, depending on the structure. The calculation progress is displayed in the progress bar, found in the bottom of the Control Panel. During the calculations, QtPISA interface may be used to inspect results calculated to the moment.

In addition to the coordinate and crystal data (both are contained in the coordinate files and PDB entries), PISA may require explicit specification of ligands that should be excluded from the analysis. This is done from the Data page, which is displayed immediately after the input of coordinated data, please see further details here. After selecting the needed ligands, PISA calculations must be re-started. This, too, is done from the Data page, and can be performed without waiting for current calculations to finish.
 

See also