P I S A
Protein Interfaces, Surfaces and Assemblies
|
P I S A |
|
Protein Interfaces, Surfaces and Assemblies
| ||
For PISA to function properly, the following directories need to be created and files placed:
| Directory | Contents | Description |
|---|---|---|
| SCRATCH | temporary files |
Scratch area for keeping temporary files |
| SRS | graph.srs index.srs struct.srs |
CCP4's Storage, Retrieaval and Search database, which contains descriptions of some 10,000 ligand (small chemical) structures. |
| MolRef | molref.idx molref.rdt |
Database with chemical properties of ligand (small chemical) structures. |
| PisaStore | agents.dat asm_params.dat intfstats.dat rcsb_symops.dat syminfo_pisa.lib |
List of common precipitation agents, parameters for free Gibbs energy calculations, statistical distributions of interface properties in the PDB, translation between symmetry operations used by CCP4 and RCSB and space symmetry group descriptions. |
| Help | index.html qtpisa-*.html qtpisa-help.css *.png |
HTML-formatted Help pages. |
These directories need to be specified in the Configuration Settings dialog, similar to one below:
The dialog can be raised by selecting the View/Settings menu item (qtpisa/Preferences on Mac OSX), by clicking on the Settings button in the Toolbar, or pressing the Ctrl-G (⌘-G on Mac OSX) hot key.
The directories may be typed directly in the corresponding fields, or specified by navigation in file system, using browse buttons on the right from the fields.
In addition to the directories, configuration includes specification of a molecular graphics viewer, which PISA may use for displaying monomeric units, interfaces and assemblies. Available options include None (visualisation switched off), Rasmol, Jmol and CCP4 MG. Set the Viewer combobox to the desired option, and specify path to the viewer in the following field. For Jmol, give path to Jmol.jar, for CCP4 MG on Mac OSX, give path to QtMG.app folder. In other cases, give path to viewer's executable.
The last configuration settings is for the interface interaction radar, which switches it from Simple to Detail mode. In the latter mode, the radar gives a more detail statistical information on the interaction value of interfaces. However, the additional information is more difficult to interpret, and expected to be useful only in rare cases. Therefore, Simple mode is the recommended one, while Detail setting should be considered as an experimental feature.
The changes actualise only when Apply button is pressed. In order to discard changes, push Cancel button. All configuration may be read from text-formatted Configuration File, which is also used for running pisa in command-prompt (GUI-less) mode. In order to read configuratuon file, push Load CFG button, and navigate to the file, after which push Apply button.
Once configured, QtPISA stores all configuration items in user's home area, and will load them automatically at next start. QtPISA may be reconfigured as many times, as necessary. Note that pushing the Apply button resets QtPISA, which erases all current calculation results.