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Collaborative Computational Project No. 4 |
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Collaborative Computational Project No. 4 |
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The CCP4 Documentation Wiki is a new way of documenting the CCP4 software, with the aim of being more accessible to GUI- and novice users:
The focus is on how to user the software through the user interface, and the wiki is divided into two main areas:
The documentation wiki is distinct from the CCP4 User Community Wiki established by Kay Diederichs:
It is intended to be a collection of crystallographic knowledge as discussed on the CCP4 mailing list, and elsewhere. It is wider in scope than CCP4 as it may contain information about anything relevant to protein crystallographers, whether methods-related ("what is the best program for purpose X?"), problem-oriented ("my crystals melt if I look at them"), or concerning hardware ("what is your opinion on robot X / computer Y?").
The distribution contains individual program documentation for all programs, both in HTML format and as formatted text (for use with the man command). It is intended that users look at the documentation locally, to ensure compatibility with the locally installed programs and to avoid network traffic. However, documentation for the latest release is also available here:
The list of programs can also be seen grouped by function:
A copy of the latest CCP4i2 documentation can be found here:
Before you start using the CCP4 suite from the command line, some directories
need to be added to the PATH and some other environment variables need to be
set. In the following instructions replace /path/to/ and <version>
with the appropriate text for your installation.
If you are happy to use the bash shell, you can obtain a correctly set up
environment by executing the script /path/to/ccp4-<version>/start
If you want to run CCP4 programs in your current shell, run
source /path/to/ccp4-<version>/bin/ccp4.setup-sh (in
bash/dash/zsh shells) or
source /path/to/ccp4-<version>/bin/ccp4.setup-csh (in csh/tcsh shells).
Windows users can get a correctly set up environment by running the CCP4Console program.
The CCP4 manual gives an overview of the CCP4 suite in the context of the structure determination process. Its content is distinct from the program documentation, and while it is becoming increasingly out-of-date it still contains useful background material.
Copies of the manual can be downloaded here:
Note that a postscript version of the manual is also distributed as part of the CCP4 suite, along with the LaTeX source code.
I am looking at preparing some graphical tutorials (inspired by some for the DNA project). Here is a simple one:
If people like the style, I will do more - Martyn.For a workshop in Japan in 2000, Liz Potterton and Martyn Winn prepared tutorials in HTML, to be used with CCP4i. These have since been developed by Maria Turkenburg with extensive help from Eleanor Dodson, Pryank Patel, Norman Stein and others, into a set of tutorials which is distributed with the suite (which is the version to use, for reasons described above). The tutorials are also available here:
More recently, some Molecular Replacement tutorials were developed for a workshop in Beijing, October 2006. For the moment, they can be found here
but will be in release 6.1 of the CCP4 suite.JLigand tutorial materials:
Eleanor Dodson prepared a document containing all the maths a protein crystallographer might come up against. It serves to have this all together, and available on the web, so Maria Turkenburg developed it further. It is distributed with the suite (which is the version to use, for reasons described above) as a set of documents in which certain symbols are represented by small .gif-pictures. This is not ideal, since a change of font by the user may make them stand out badly from the text. It is recommended to view the documents with 12pt Times and 10pt Courier fonts. They are also available here:
As well as information on how to use the programs, the individual program documentation in the CCP4 installation contains background information on the science behind the programs, which is well worth reading.
Certain topics warrant a document dedicated to them. Examples of these are: re-indexing, twinning, alternate origins, cheshire cells, symmetry, and density modification. These are distributed with the suite in the 'General' section of the documentation (which is the version to use for reasons described above), and are also available here:
'Roadmaps' are an excellent way to get an overview of the processes involved in macromolecular structure determination and the use of CCP4 programs therein. The current recommended roadmaps through the CCP4 suite have been produced by Maria Turkenburg and are distributed with the suite (from version 4.1.1). They are also available here:
Kevin Cowtan had previously produced the following roadmaps showing which programs may be useful in various stages of the structure determination (these roadmaps are unsupported and may now be slightly dated...).
There was also a small selection of hyperlinked roadmaps:
Here are some talks given by CCP4 staff which may be useful:
