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News of the CCP4I Documentation and Tutorials

Maria Turkenburg (
January 1999

CCP4 web logo CCP4I: Graphical User Interface

CCP4I Documentation

With the official release of the CCP4 Interface (CCP4I, for short), there will be a comprehensive package of documentation, written in HTML, and included with the CCP4 release at a level similar to the CCP4 Program Documentation. The documentation as it stands today, is already available in York, where it is being written by me, Maria Turkenburg, and where the Interface itself is being written by Liz Potterton (see News of Progress on the CCP4 Graphical User Interface - CCP4 Newsletter July 1998).


After an introductory page, the documentation can be viewed with or without frames, to suit everybody's browser and personal preferences. In the frames version, there is a navigation bar on the left, containing a list of all available documents. This list is also shown when you try to enter the frames version in a frames incapable browser. Furthermore, there are navigation buttons, which get you through the whole set of documents one by one.

The first section of the documentation contains General information on the runnings of the Interface, explaining the philosophy and its features. This section is ready for release. I will keep adapting it as new features are added to the Interface.

While testing the Interface Modules and Tasks, I write the documentation for the next sections (describing the Interface Modules and Interface Tasks), adding to and adapting the pieces Liz writes. There is specific information on the Task Window Layout, highlighting the parts the user is most-advised to look at. In addition, these sections have a more detailed description of the Interface and the programs it is running. I have included cross-references to the CCP4 Program Documentation and any other appropriate information I could find, in the form of clickable links.

Certain aspects of the documentation, written together with Eleanor Dodson, have grown into separate entities, directly related to specific problems in crystallographic structure solution. They are: reindexing, twinning, handling of FreeR sets in conjunction with UNIQUEIFY, and choosing the right scaling program (the last one straight from a tutorial by Ian Tickle). There has been a call to make them available in advance of the official release of the Interface. I have created a Specialist Help section in the Interface Documentation, which is now available through my lab web pages.

Self-contained tutorial material written in HTML by other people, has been included in a section called External Special Help. This contains the complete Isomorphous Replacement tutorial from the Bath School (by Ian Tickle) and links to Kevin Cowtan's dm Workshop, Structure Factor Tutorial and Fourier Book. I am now working on including the Molecular Replacement tutorial from the Bath School (also by Ian Tickle), too.

The last section of the documentation contains the Tutorials (see below) and Documentation for Programmers.


The colours I have chosen, are based on the Interface and CCP4 colours. Starting from the main colour of the Interface as a background for the documents, and with the official CCP4 weblogo included in every page, it needed another colour to balance the scheme. It turned out that the information on colour wheels and colour theory I found on the web, was a great help. That is where the reds come in. A rosy red for the titles, and a dark brown-red for visited links.


I have put those parts of the Documentation which I consider to be separate, i.e. the External Special Help, the tutorials, the documentation for programmers, and the CCP4 program documentation, in separate browser windows. And, to be able to read the tutorials while carrying out some of the actions, it may be necessary to open extra browser windows. This might not suit everybody, but I have tried to make it as painless as possible.

CCP4I Tutorials

A guided tour of the Interface, solving and refining RNAse SA on the way!

The tutorials are intended to be stand-alone entities, representing the various stages of a crystallographic structure solution, and can be worked through separately. At the beginning of every tutorial is a section describing the directories and files needed for that particular tutorial. Pre-prepared files for various stages will be available from $CEXAM.

In these tutorials, actions you are required to perform will be displayed in bold CCP4bluegrey letters.

The first tutorial is concerned with setting up and getting organised, and deals with the 'Utility' features of the Interface, i.e. the Database, the FileViewer etc.

Future plan

In conjunction with CCP4 Program developers, more documentation will be developed on the output of the programs. I will need lots of help with this!

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