CCP4i: Graphical User Interface
	Tutorial 1

Setting up and getting organised

Looking at files

After Preparing data you now have a number of files you can look at. Most of these are listed in the "View Files from Job" pop-up menu in the Database menu on the right-hand side of the Main Window. This list refers to the most recently run job, unless you pick one specifically. The options are as follows:

View Log File

To list the usual CCP4 Program log file (which is on the 'current project' directory, unless you have chosen to put log files elsewhere, through the Directories&ProjectDir window), which has a few CCP4i-specific lines at the top and bottom.
Select View Log File
and the log file is shown in a FileViewer window.
It can be searched by clicking the Find button and typing a string, e.g. status.
Click Highlight
to activate the search,
and use the Next and Previous buttons
to find the matches, the last one of which states the "TERMINATION STATUS" of the Interface.
Click Close Find and Quit
to end the FileViewer session.

View Log Graphs

To view potential graphs from the log file through the Loggraph Utility. Many CCP4 programs output tables of data in their log files, which can be interpreted and displayed as graphs. Unfortunately for this tutorial, the Import task, which you have run to prepare the RNAse SA data, does not have any graphs.
If you want to see what Loggraph can do, type loggraph $CEXAM/tutorial/REFINE/refmac.log
outside the Interface.

View Command Scripts

To view the command files through the FileViewer Utility. The command files are temporary (.tmp) files on the TEMPORARY directory, which are gathered together into a file called "scripts_job-number.tmp". The same information can be found in the .run and .def files (see below) which the Interface uses directly. The Find tools work as before.

Input files .. rnase25.na4

The Import Task has only one input file. It is shown through the FileViewer, and can be searched with the Find tools.

Output files .. rnase25.mtz

The Import output file is shown through the FileViewer, after the Interface has run MTZDMP on it, and can be searched with the Find tools.

In addition to these, are the .run file on the TEMPORARY directory and the .def file on ccp4itut/CCP4_DATABASE. For these,
click the View Any File button
just above the Database Menu. Then

.run	.def
Select directory TEMPORARY	Select directory ccp4itut
Click ccp4itut_job-number_import.run	Select CCP4_DATABASE
Click OK	Click job-number_import.def
	Click OK

If this is your first Interface session, the job-number is 1. Double-clicking the filename has the same effect as clicking OK after clicking the filename once. The files are shown through the FileViewer, and can be searched with the Find tools as before.

More information

If you want to know more about the files the Interface generates,
look at the documentation
for Introduction and Configuration, and, if you are really adventurous, the Documentation for Programmers.

The Interface documentation on features from this tutorial can be found at: