Current release is v5.0
Next release is CCP4 v6.0 (Ingleton): http://www.ccp4.ac.uk/dev/releases.html
When will the next release be available? CCP4 v6.0 is currently in testing, and a test version is available now from the link above. We are also currently waiting for an update to the academic licence.
What's the situation with the licence? The academic licence for CCP4 v5.0* expired on 31st March this year, and negotiations within CCLRC (the organisation that supports CCP4) have so far failed to produce a satisfactory update that can be made available.
When a new licence is available then it will be announced publically via the website and bulletin boards. The next release of CCP4 will also require the submission of a new licence agreement. Unfortunately we will not be able to contact existing licence holders individually to advise them of the update.
Regarding licensing of the current release the official position is that there is no valid licence. However being pragmatic, we are proceeding on a "don't ask, don't tell" basis and note only that the software is still available for download.
Alternatively contact the chairman of CCP4 Jim Naismith directly, see http://www.ccp4.ac.uk/staff/staff.html.
CCP4 documentation: http://www.ccp4.ac.uk/ccp4/html/phaser.html
Phaser website: http://www-structmed.cimr.cam.ac.uk/phaser/
What they say: "Phaser is a program for phasing macromolecular crystal structures with maximum likelihood methods. It currently has methods for brute force and fast likelihood-based rotation and translation functions for molecular replacement. Methods for experimental phasing are under development."
Anything else? Currently does molecular replacement - next major update will also deal with heavy atom substructure solution.
How do I learn how to use it? There is a tutorial available via the Phaser FAQ: http://www-structmed.cimr.cam.ac.uk/phaser/faq.html
Phil Jeffrey's email (& he is at Princeton, hmm)Clipper Libraries: http://www.ysbl.york.ac.uk/~cowtan/clipper/clipper.html
CCP4 documentation: http://www.ccp4.ac.uk/ccp4/html/cpirate.html
Pirate webpages: http://www.ysbl.york.ac.uk/~cowtan/pirate/pirate.html
What they say: "Pirate: Phase Improvement Requires Another Tenuous Eponym - Pirate is a new statistical phase improvement program [that] performs statistical phase improvement by classifying the electron density map by sparseness/denseness and order/disorder, with the aim of obtaining superior results to conventional solvent mask based methods without requiring knowledge of the solvent content."
Anything else? pirate is a replacement for DM, and requires that target distributions using a known ('reference') structure for which calculated phases are available. The method is dependent on the reference structure being a good match to the features of the unknown ('work') structure. For the common case of a protein of mostly equal atoms (i.e. not a metalloprotein), a single reference structure can be used, with modifications automatically applied to the reference structure to match its features to the work structure. It is also possible for pirate to evaluate several reference structures in order to pick the best one.
Suitable reference structures can be constructed from the PDB using "cmakereference".
CCP4MG website: http://www.ysbl.york.ac.uk/~lizp/molgraphics.html
What they say: not a lot.
Anything else? GGP4MG is the CCP4 Molecular Graphics project. CCP4MG can currently view coordinates (in PDB or mmCIF formats), show surfaces (including electrostatic surfaces), superpose protein structures (homologous and non-homologous), generate and display electron density maps and packing diagrams, and creating publication-quality pictures and movies.
How do I learn how to use it? There is a tutorial included in the CCP4MG documentation which is installed as part of the package, and is easily accessed from the "Help" button.
COOT website: http://www.ysbl.york.ac.uk/~emsley/coot/
What they say: "Displays maps and models and allows certain model manipulations: idealization, real space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers, Ramachandran plots, model validation and other stuff."
Anything else? Coot is part of the CCP4 Molecular Graphics Project. The Molecular Graphics Project has a wide remit and crystallographic map fitting is a part of that. The Coot functions have their own interface and some of them will be integrated into CCP4mg in due course.
How do I learn how to use it? There is a tutorial in Postscript format at http://www.ysbl.york.ac.uk/~emsley/coot/tutorial.ps.
CRANK website: http://www.bfsc.leidenuniv.nl/software/crank
What they say: "CRANK is a new suite of programs for automated macromolecular structure solution. It uses an XML based framework to join many different crystallography programs into a unified whole. CRANK is intimately linked to the CCP4 package, using CCP4i for job setup and control."
Anything else? Currently, Crank has support for SAD, SIR and SIRAS experiments. Support for MAD and MIR(AS) is being added. The Crank package includes BP3 and CRUNCH2:
With these two programs, along with DM from the CCP4 suite, Crank is a fully functional suite and allows the solution of macromolecular structures up to the point of density modification.
How do I learn how to use it? There is a SAD tutorial on the CRANK website: http://www.bfsc.leidenuniv.nl/software/crank/tutorial/tutorial-sad.html
CCP4i has a number of updates:
plus a large number of bug fixes and minor improvements to usability and functionality.
Chooch is a program by Gwyndaf Evans that produces f' and f" curves from a fluorescence energy scan. It calculates the position of the peak and inflection point of the absorption edge and estimates f" at the peak and f' at the inflection point.
SUPERPOSE performs structural alignment based on secondary structure matching. Given two structures, the program reports the transformation matrix required to move one to the other, and a residue-by-residue listing of the alignment (including the quality of the match, and identification of strands and helices).
New coordinate functions are available in the PDBCUR program. The new functions include:
ab initio procedure for the determination of protein structure using atomic resolution data, and for finding sub-structures from anomalous or isomorphous differences.
How do you search for multiple molecules?
Eleanor says: After the first translation function choose the most hopeful solutions - it depends on how good they are whether you take 10 or 100, then [in] the GUI:
Selection translation
Input the rot.mr
Add known solutions
then give the edited tran1.mr
and search again - you will then get solutions labelled:
SOLUTIONTF1 ...
SOLUTIONTF2 ...
And you repeat this procedure for 3/4/5 etc molecules..
MOLREP is more automated but only selects the "best" 1st, 2nd etc translation so sometimes fails to get a solution where Amore can succeed.
Or you can use PHASER which is also very automated and searches till it finds the request no of molecules..
See http://www.ccp4.ac.uk/ccp4_projects.html
Automating CCP4 software
E-science Resource for High Throughput Protein Crystallography
http://clyde.dl.ac.uk/e-htpx/index.htm
Biocrystallography (X) on a Highly Integrated Technology Platform for European Structural Genomics
http://www.ccp4.ac.uk/projects/bioxhit.html
Protein Information Management System
Automating the collection and processing of X-Ray protein crystallography data