CCP4i: Graphical User Interface
	Tutorial 1

Setting up and getting organised

Before you start

For this first tutorial, which is most useful for first-time users of the Interface, you only need what is described in the Introduction:
a directory called "ccp4itut".

It is also advisable to
start a Netscape session by typing netscape (you may have to specify a version, e.g. netscape30 or netscape4.05)
before entering the Interface.

Directory selection

CCP4i expects users to keep all the files relating to one project in one directory called 'the Project directory'. The Interface will create a sub-directory of the project directory, called "CCP4_DATABASE", in which it keeps its own files. You are free to decide what exactly is one project, but it should probably be one structure solution, and you may have more than one project in progress at one time.
The Interface also has the concept of directory aliases, which work similarly to Unix environment variables: you provide a short one-word alias for the long pathnames of project directories and also, optionally, for other directories you use regularly.

Hints on using Interface windows:
The "Directories&ProjectDir" window may look a little confusing at first. Here are some hints to features seen throughout the Interface -
try them out
while going through the actual tutorial.

• You can jump from one field to the next by using the 'Tab' button on your keyboard, or by pressing 'Enter'. As soon as you start typing a directory or file name, the field will turn a gold colour like the background colour of the document you are reading now. When you have finished typing, press return, or click the left mouse button outside the field, and the field will turn white as a sign that the Interface can find the directory/filename you are pointing to. The gold colour remains if the user input is wrong (e.g. input file which does not exist). This is a feature of the Interface, and you should use it to your advantage.
• When you click on a grey button, Something Will Happen. The grey colouring indicates that the button controls window management rather than it being a data option. For example, the button labelled "Browse" will bring up a
  "File or Directory Selection" window. This window has a facility to "Go up a directory", and lists of subdirectories (on the left) and files (on the right) in the 'Current directory'.
• (Pop-up) Menu buttons are indicated as such by a small rectantangle at the right hand side of the button. If you hold the left mouse button down when the cursor is over a menu button, the corresponding menu will be displayed. For example, the bottom line of the "Directories&ProjectDir" window has menu options on where to write log files.
• Extending frames are used where you might want to enter variable amounts of information. For example, if you click the buttons 'Add project' or 'Add directory alias' in the "Directories&ProjectDir" window, an extra line will be created in the window for you to define extra projects or extra directory aliases. Next to these buttons is a menu button labelled "Edit list" which has options to edit the data by removing a line which is no longer required, or copying a line. You select the line to copy/delete by clicking in an entry field (i.e. a field which allows you to type in something rather than a menu or button) with the right mouse button. If you use this option, read the instructions in the Message line (the gold-coloured line at the top of the window).

	If you are using the Interface for the first time	If this is not the first time you are using the Interface
1	Upon typing ccp4i the Interface will bring up the Main Window automatically or (if your shell setup is such) bring up the shape of the Main Window which you can place on your screen where you want it.
2	A window called "Directories and Project Directory" will come up in the same way. The Interface has created a file "directories.def" in the directory .CCP4/unix/ (or .CCP4/windows/, where .CCP4/ is a subdirectory of the user's home directory), where it will store your directory choices/aliases.	There already is a file "directories.def" in your .CCP4/unix/ and/or .CCP4/windows/ directory. Click on the Directories&ProjectDir button near the top right of the Main Window to bring up the "Directories and Project Directory" window.
3	Click in the field "Project", type ccp4itut as your first alias, and make it point to ~/ccp4itut in the field "uses directory:". See above for hints on how to do this.	Click on Add project, type ccp4itut and make it point to ~/ccp4itut
4	The Interface has entered this directory in the 'Project for this session of CCP4Interface' pop-up menu.
5	Since there is only one possible Project directory, this is automatically installed for this session.	Click on the pop-up menu button for the 'Project for this session' and select ccp4itut
6	Click on Apply
7	The Interface brings up another window, called "Create". Read this carefully. The Interface is installing "ccp4itut" as your Project Directory, and wants to create a database directory for this, where it will keep track of all the things you do while working on your current project. Click on Create Directory The Interface has created a subdirectory of "ccp4itut", called "CCP4_DATABASE".	Since you have used the Interface before, you have probably created a database before. If not, proceed following the left-hand-side of this table.
8	Click on the Add directory alias button. In the field "Alias:", type rnase_exam and make it point to $CEXAM/rnase/ Please note that the aliases must be one word, with only alphanumeric characters and underscores. Any other character will be converted to an underscore, and you will be warned of this.
9	Click on Apply&Exit

N.B. In cases where the process the Interface is trying to perform takes a fair amount of time, a small message window will come up (either automatically, or just the shape of one you can place yourself, as before). This window tells you what the Interface is trying to do.

More information

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