The CCP4 Core Group is very pleased to announce the release of the latest version of the CCP4 Software Suite. Version 7.1 (Skipton) is now available from the CCP4 download website. The release is available for all MS Windows, Linux and Mac OSX platforms.
While CCP4 7.0 can be kept on your computers for as long as necessary and in parallel to CCP4 7.1 (Mac OSX and Linux only), we encourage all our users to switch over at first convenience because:
CCP4 Release 7.1 comes as a complete modernisation of version 7.0, which have seen the longest life time ever in CCP4 history, being released more than 4 years ago and complemented with 79 updates. However, changes in operating systems and advances in computer languages, accumulated over this significant time period, have made it necessary to introduce technical modifications, such as progressing to C++-11, that could not be carried out using the CCP4 update system.
CCP4 7.1 represents the final state of 7.0 update series, complemented with newest versions of many important components, for example:
The latest version of Interactive Model Building Software from Dr. Paul Emsley, MRC/LMB, Cambridge, with many improvements and new features.
Currently available only for Mac OSX and Linux users. The corresponding update for Windows systems will be issued as soon as feasible
Diffraction image processing software from Diamond Light Source Ltd., CCP4 and the Lawrence Berkeley National Laboratory. DIALS now includes a scaling module and improved multi-crystal symmetry tools.
A Graphical User Interface for DIALS programs.
Automated diffraction image processing using an expert system.
Maximum likelihood structure solution software from the group of Prof. Randy Read, Cambridge.
SHELX Software from Prof. George Sheldrick, University of Goettingen, Germany (SHELXE is supported by Dr. Isabel Uson, Barcelona, Spain)
BUCCANEER Software from Dr. Kevin Cowtan, University of York, UK, with important fixes and improvements
and many others. CCP4 continues to provide
Automated Model Building Software from Dr. Victor Lamzin, EMBL Outstation in Hamburg, Germany integrated with the CCP4 Core package.
In CCP4 7.1, you will find considerably advanced and improved:
CCP4 Graphical Interface with many tasks and report pages revised and partly redesigned, numerous bugs fixed and overall stability enhanced. In particular, CCP4i2 now contains the deposition module, which allows you to prepare files in mmCIF format, suitable for deposition to the PDB in a fairly automated manner.
In addition to numerous modifications, advances and updates, CCP4 7.1 introduces a few brand new components:
C++/Python application and library for handling coordinate and reflection data (from Marcin Wojdyr, Global Phasing Ltd., Cambridge, UK)
GEMMI is a highly efficient and sophisticated package for manipulating coordinate and reflection data in various formats (such as .pdb, .mmcif, .mtz). The package is very useful for developing MX-related applications in C++ and Python.
Assistant application for making and analysing search models for Molecular Replacement (from the group of Prof. Daniel Rigden, University of Liverpool, UK)
MRparse finds suitable structure homologs, aligns and represents them graphically for reference and more efficient MR ensembling. Available in CCP4i2 interface.
A framework for distributed CCP4 Computation
CCP4 Cloud represents a conceptually new approach to organising and maintaining crystallographic projects in CCP4 and running CCP4 tasks. With this system, you can keep all your data and projects in the Cloud and manage them using any modern browser running on a desktop PC, laptop, tablet/ipad or even a smartphone, from any geographic location. In CCP4 Cloud, only the initial data need to be uploaded once; within a Project, the data is passed from task to task behind the scenes, without exchange with the client device. CCP4 Cloud represents Projects as branched trees, making the structure solution pathway perfectly transparent and easily reconcilable. All main stages of structure solution in MX: image processing, phasing, model building, refinement, validation and PDB deposition are presented in CCP4 Cloud as a collection of more than 75 tasks. Interactive tasks, such as Coot, are also available in CCP4 Cloud. Using such tasks requires a local CCP4 7.1 setup, which contains the CCP4 Cloud Client, a piece of software linking CCP4 Cloud with Coot installed locally. Just double-click on the CCP4 Cloud Client icon (CCP4 Diamond with a cloud and wireless sign) in order to start using CCP4 Cloud right after installation of CCP4 7.1 (you will be required to register as CCP4 Cloud user first time).
The CCP4 Core Group will be happy to help anyone to start using CCP4 Cloud. Development of CCP4 Cloud was supported by BBSRC UK Grant BB/L007037/1 and is a result of a collaborative effort of many developers and enthusiasts.
Automated model builder (from Eugene Krissinel and Andrey Lebedev, CCP4 Core Group)
CCP4build combines several applications: CParrot, CBuccaneer, Refmac, Coot and EDStats, for the enhancement of automatic model building in CCP4. CCP4build explores several model building scenarios in an iterative approach with rollbacks, and adjusts automatically to building in both experimental phases and phases obtained in the course of molecular replacement. CCP4build is available in CCP4 Cloud.
Interface to BUSTER software from Global Phasing Ltd.
The interface allows a user to refine macromolecular structures with BUSTER software from Global Phasing Ltd. The interface is available through the CCP4 Cloud - both in your own installation as well as through the CCP4 Cloud service at RC Harwell (UK).
The latter case requires online authorisation for academic users with Global Phasing Ltd. (which are kindly providing the software to all academic users free of charge), which is done via an authorisation facility found in user’s account settings. Use of the interface within your local CCP4 Cloud installation requires a separate, local installation from www.globalphasing.com.
For Mac OSX and Linux platforms, on-line setup through the CCP4 Setup Manager is the recommended option. CCP4 Setup Manager enables you to choose a desirable set of components, download, install and configure them automatically.
Before installing CCP4 7.1, PLEASE MAKE SURE THAT NO CCP4 PROGRAMS ARE RUNNING, PARTICULARLY CCP4i AND CCP4i2. The simplest way to achieve that is to REBOOT YOUR COMPUTER BEFORE THE INSTALLATION OF CCP4.
Installation on MS Windows systems requires downloading the whole package as an executable installer and running it on your machine. Be prepared to see a warning message from MS Windows, suggesting that the software may be harmful for your system – please trust CCP4 and choose “install anyway”. It is necessary that you REBOOT YOUR WINDOWS PC AFTER INSTALLATION, before attempting to run any of CCP4 programs.
We advise you to always include Coot in your installation package and install it simultaneously with the rest of CCP4. If you intend to use Coot from other sources, be prepared to link it with CCP4 after installation and manage it separately. CCP4 cannot provide updates to Software installed from sources other than CCP4 and cannot guarantee a flawless integration of such software – although we will do our best in order to resolve any issues you may encounter.
Please note that, starting from CCP4 7.1, 32-bit packages are no longer available.
We would like to thank all of the developers who have contributed to CCP4 7.1, and all of those who have helped in testing it. The following publication should be used to cite the use of CCP4:
M. D. Winn, C. C. Ballard, K. D. Cowtan, E. J. Dodson, P. Emsley, P. R. Evans, R. M. Keegan, E. B. Krissinel, A. G. W. Leslie, A. McCoy, S. J. McNicholas, G. N. Murshudov, N. S. Pannu, E. A. Potterton, H. R. Powell, R. J. Read, A. Vagin and K. S. Wilson (2011) Overview of the CCP4 suite and current developments, Acta Cryst D67 235-242.
Use of individual CCP4 programs should be acknowledged also by the citation of respective publications, where required (please cf. from program documentation). CCP4 is supported by the BBSRC UK through grant BB/S006974/1 (CCP4 Advanced Integrated Approaches to Macromolecular Structure Determination), as well as by our industrial users.
CCP4 7.1 is out now. A considerable effort has been put into developing, compiling, bundling and testing its many new components and underlying libraries. Despite all the effort we've made, bugs and unforeseen “features” will most certainly be found in the Suite, which has grown substantially in size. When bugs and errors are discovered, the best way to deal with them is to report them to us at ccp4@stfc.ac.uk. We value highly all feedback from our users, and together we will bring CCP4 yet closer to community expectations and standards.
Many thanks for being CCP4 users,
Eugene Krissinel
on behalf of CCP4 Core Group:
Charles Ballard
Andrey Lebedev
Ronan Keegan
David Waterman
Kyle Stevenson
Ville Uski
Oleg Kovalevskiy
Tarik Drevon
Karen McIntyre