News of CCP4 Release 6.1
, Martyn Winn, Charles
Ballard, Francois Remacle, Norman Stein and Ronan Keegan
CCP4, CSE Department, STFC Daresbury Laboratory, Warrington WA4 4AD
The current release of the CCP4 software suite is version 6.0.2, which was
made available in December 2006 and which has previously been described in some
detail in an
article in newsletter 44. This article outlines the new and updated
programs and features that are currently scheduled for inclusion in the next
major release of CCP4, version 6.1, due out later in 2008.
2 Major Changes in CCP4 6.1
2.1 New programs
A number of significant new programs will be included in CCP4 6.1:
- AFRO: a program for calculating EA values (the
normalised heavy atom contribution) from SAD, MAD and SIRAS data.
- BUCCANEER: statistical model building program that can be used to
trace protein structures in electron density maps by identifying connected
alpha-carbon positions using a likelihood-based density target.
- CTRUNCATE: a program for converting intensities to structure
factors and checking data quality. CTRUNCATE is
intended to supersede the existing TRUNCATE program.
- CRUNCH2: program for determining the substructure of the
anomalous scatterers or heavy atoms.
- MrBUMP: an automated pipeline for molecular replacement developed
by Ronan Keegan and Martyn Winn, which includes search model retrieval
and search model preparation.
- PISA: a standalone version of Eugene Krissinel's PISA (Protein
Interfaces, Surfaces and Assemblies) program that is a useful for
examining various characteristics of protein packing and other
interactions. Previously the PISA functionality was only available as a
web-based service from the EBI.
- POINTLESS: program for Laue and Patterson group determination from
unmerged reflection data, as well as a number of subsidiary functions
including: reflection format conversion, checking and reindexing of
reflection data against a reference set, and apply a pre-selected
- RAPPER: program for generating protein conformers by discrete
sampling of likely conformers within a given set of restraints. It can
be applied to a number of problems, for example: ab initio loop
building, comparative modelling and Cα-trace modelling. It can also
be used to build and refine conformers using X-ray crystallographic
The RAMPAGE module of RAPPER also provides an analysis tool that
generates Ramachandran plots which are more consistent with current
models than those in PROCHECK.
- SEQUINS: SEQUence INSertion detection program that performs
sequence validation by comparing model side chains against electron
density. It can be used after molecular replacement or to validate
structures in the PDB.
- XIA2: an expert system for performing automated reduction and
analysis of X-ray diffraction image data with minimal user input. It is
aimed at two principal sets of users: novice users with little knowledge
or experience of data processing, and expert users who wish to process
higher volumes of data.
There are also new utility programs scheduled for inclusion:
- IDIFFDISP: a standalone viewer for raw diffraction images which is
intended as a replacement for the old IPDISP program.
- MTZ2CIF: a utility that generates mmCIF reflection files suitable
for deposition, and is intended to replace OUTPUT CIF option of
- R500: utility for correcting REMARK 500 lines in PDB files
before submission to a deposition site.
- SEQWT: a program that estimates protein molecular weight from
- SYMCONV: a utility for interrogating the CCP4 symmetry
libraries in order to look up information about spacegroups and
symmetry operations in various formats.
- BAUBLES: a utility for re-rendering CCP4 log files into
HTML markup. Baubles will be integrated into CCP4i.
It should be noted that many of these programs have been available
for some time already, either via the CCP4 Prerelease Pages at
or via their own project-specific pages. However, their inclusion in
CCP4 6.1 means that users will no longer have to download and install
2.2 Updated Programs
In addition to the new programs outlined in the previous section there
are various updates to many of the existing programs in the suite. These
- PHASER 2.1.2 (this version covers MR, SAD and combined MR and
- REFMAC 5.4.0067
- SCALA 3.3.1
- SFCHECK 7.02.6
- MOLREP 10.1.7
- MOSFLM 7.0.2 (along with the new iMOSFLM interface)
- OASIS updated to OASIS-2006
- PDB_EXTRACT 3.0
- CRANK 1.20
Please note that these version numbers are correct at the time of
writing but may be superseded by newer versions before CCP4 6.1 is
finally released. The latest versions of COOT and CCP4MG will also be
made available for download with CCP4 6.1.
2.3 Changes to Graphical User Interface CCP4i
The improvements and changes to CCP4i are described extensively
elsewhere in this newsletter. They include
new task interfaces for the new programs plus many new core features
2.4 New Libraries
The release of CCP4 6.1 will include the new DiffractionImage
library, which provides a set of C++ functions (plus wrappers in different
languages including Tcl and Python) for handling diffraction image data
from a variety of sources.
DiffractionImage also comes with a set of utility programs:
- diffdump: displays all the "standard" information from a
specific diffraction image file
- printpeaks: prints a list of peaks found on an image
- automask: automatically generate a backstop mask from a
- diff2jpeg: generate a JPEG from an image file
2.5 Deprecated and Withdrawn Programs
As part of the CCP4 6.1 release a number of programs have been
designated as "deprecated", in anticipation of removing them
completely from future releases. These programs have either been
superseded by superior programs, or have fallen out of mainstream
use. They are:
- BEAST (replaced by Phaser)
- ROTAPREP (replaced by Combat)
- ARP_WATERS (the latest version of ARP/wARP should be used instead)
- XLOGGRAPH (replaced by loggraph)
- IPDISP (replaced by idiffdisp)
- BPLOT, POLYPOSE, RSEARCH, RESTRAIN,
XDLMAPMAN and XDLDATAMAN
The source code of deprecated programs will still be included for
download, however they will not be built as part of the standard
installation process and will not be included in the binary
distributions that CCP4 provides.
2.6 Other changes and new features
There are various miscellaneous changes and features scheduled for
Dependency on Fortran 90
The latest versions of REFMAC (5.3+) and MOLREP (10+) now require a
Fortran 90 compiler in order to build. This should only affect users
who build the suite from source code.
The CCP4 configure will check for Fortran 90 support and will
automatically disable the REFMAC and MOLREP builds if it is not
Update Alert Mechanism
It is intended to implement an "update alert mechanism" as
part of CCP4 6.1, which will automatically notify users when bug
fixes or updated program versions become available on the CCP4
server. Although the details are still being worked out, the
intention is to help users keep their CCP4 distributions more
up-to-date in between major releases of the suite.
InstallShield installation wizard for Linux systems
For CCP4 6.1 an InstallShield-based installer (similar to that
already used for Microsoft Windows platforms) will be available
for installing pre-compiled executables onto Linux systems.
3 Current Status and Availability
At the time of writing (January 2008) there are currently still a few
components and features which have not yet been fully integrated into the
suite, however initial test versions have been made and are undergoing
testing with a selected group of developers and users.
It is planned that a small number of additional test releases will be
made over the next couple of months ahead of the full public release. If
you are interested in trying out a trial version of 6.1 then please
CCP4 6.1 is scheduled for a full public release sometime in spring 2008.
Watch for announcements on the CCP4bb
mailing list and other crystallographic lists, or check the
CCP4 home page for news.
Finally, this article reflects our current state of knowledge about
the expected content of CCP4 6.1, however it is possible that there may
be some changes before the public release. It is recommended therefore
that you check the list of significant changes that is distributed
with the suite and linked from the main documentation index.
The CCP4 project is a collaborative effort and continues to thrive through
generous contributions of time, energy and software from members of the UK and
international PX communities. Unfortunately time and space do not permit the
acknowledgement here of all these valuable contributions, however a list of
acknowledgements is included in the current release, and acknowledgements for
the specific developments described in this article are given below:
- AFRO is developed by Navraj Pannu; CRUNCH2 is developed by
Jan Pieter Abrahams (Leiden University)
- BUCCANEER and SEQUINS are developed by Kevin Cowtan (University of
- CTRUNCATE is developed by Norman Stein (CCP4, Daresbury Laboratory)
- MrBump is developed by Ronan Keegan and Martyn Winn (CCP4, Daresbury
- PISA is developed by Eugene Krissinel (MSD-EBI)
- SCALA and POINTLESS are developed by Phil Evans (MRC-LMB Cambridge).
- RAPPER is developed by Nicholas Furnham, Paul de Bakker, Mark
DePristo, Reshma Shetty, Swanand Gore and Tom Blundell (University of
- XIA2 is developed by Graeme Winter (CSE, Daresbury Laboratory)
- IDIFFDISP is developed by Francois Remacle (CCP4, Daresbury
Laboratory). The DiffractionImage library is developed by Francois
Remacle in collaboration with Graeme Winter.
- MTZ2CIF and SYMCONV are developed by Peter Briggs. BAUBLES has been
developed by Peter Briggs in collaboration with Kevin Cowtan and Phil
- R500 is developed by Kim Henrick (MSD-EBI)
- SEQWT is developed by Eleanor Dodson (University of York)
- PHASER is developed by Randy Read's group (Wellcome Trust,
- REFMAC5 is developed by Garib Murshudov's group (University of
- SFCHECK and MOLREP are developed by Alexei Vagin (University of
- OASIS is developed by Tao Zhang et al (Beijing National
Laboratory for Condensed Matter Physics) and Quan Hao (Cornell
- PDB_EXTRACT is developed by Huanwang Yang (RCSB PDB)
- CRANK is developed by Navraj Pannu (Leiden University)
- CCP4mg is developed by Liz Potterton and Stuart McNicholas
- COOT is developed by Paul Emsley (Oxford University)
- MOSFLM is developed by Harry Powell and Andrew Leslie; iMOSFLM is
currently developed by Luke Kontogiannis (MRC-LMB Cambridge)
- CCP4i is maintained and developed by the CCP4 group at Daresbury
The CCP4 suite is maintained, developed and released by the CCP4 group
in the Computational Science and Engineering Department (CSED) at STFC Daresbury
Laboratory, and comprises Charles Ballard, Peter Briggs, Maeri Howard, Ronan
Keegan, Francois Remacle, Norman Stein and Martyn Winn.
The CCP4 project is supported by the BBSRC, by income from commercial
distribution of the software, and by STFC Daresbury Laboratory. CCP4 would
also like to thank the many people past and present who support the project,
both with their time and with their contributions to the software suite
itself - without which the project would not be able to exist.