Dear CCP4 Users,
The CCP4 Core Group is very pleased to announce the release of the latest version of the CCP4 Software Suite. Version 6.4.0 (Long Preston) is now available from the CCP4 download website: http://www.ccp4.ac.uk/download.php<http://www.ccp4.ac.uk/download/> The release is available for Linux, Mac OSX and Windows platforms. The release mostly consolidates updates in the CCP4 6.3.0 update series, but also introduces a number of technical improvements and new features. 1. New Components and Updates (please see list of new features in individual programs documentation) New: QtRView (Generic graphical result viewer) ccp4um (Integrated CCP4 updater) QtPISA (Graphical front-end to PISA software) Updated: Phaser v2.5.5 (Molecular Replacement and Experimental Phasing) Refmac v5.8.0048 (Macromolecular refinement) CTruncate v1.13.0 (Intensity to amplitude conversion and reflection data statistics) Aimless v0.2.1 (Scaling multiple observations of reflections) Pointless v1.8.4 (Laue group determination) Xia2 v0.3.6.1 (Automated data processing) Dimple v1.2 (Automated difference map calculations) Libcheck v5.2.01 (Monomer library management program) Superpose v1.0.3 (Now includes multiple structure alignment) Ample stable (ab initio molecular replacement) CCP4mg v2.7.3 (CCP4 Molecular Graphics, much improved on features and stability) Coot v0.7.2 (Interactive model building; v0.7.1 on Windows) Arp/wArp v7.4 (Model building suite from EMBL- Hamburg) CCP4 Graphical User Interface: * multiple bug fixes * incremental changes to accommodate new programs and program updates * import from imosflm quickscale * crossec interface for estimation on anomalous scattering 2. Important technical changes CCP4 6.4.0 is released on the back of significant changes in CCP4 repositories, build and distribution mechanisms. On the user side, these changes are reflected in the following: 2.1 Coot is now integrated with CCP4 core on Linux and Mac OSX. This means, that for the first time, we distribute portable Coot, which is expected to work on all Linuxes. This also means that Coot updates through CCP4 update mechanism are now possible. Coot may be launched by typing ‘coot’ in CCP4-sourced environment in OS terminal, or, if CCP4 Setup Manager was used for installation, by clicking ‘Coot’ icon on your desktop. On Mac OSX, Coot icon is placed within the ccp4-6.4.0 directory. 2.2 CCP4 Update manager, ccp4um, is now integrated with the Suite and does not require a separate installation as an add-on feature. Updates are now possible for all CCP4 ‘external’ components (including Coot, CCP4 MG and Arp/wArp), provided that they have been installed in the same master root as CCP4. To ensure that, users are advised to use CCP4 Setup Manager for the installation of CCP4 on Linux and Mac OSX. Using CCP4 Setup Manager also ensures that the latest updates are applied at time of installation. Next, CCP4 Update Manager can be now run in the command-prompt (non-graphical) mode, in order to ease the life of system administrators. The corresponding command is ‘ccp4um -auto’. 2.3 Source code distribution of the suite has undergone considerable changes. For Release 6.4.0, CCP4 offers 3 ways to build the Suite from source code: a) the “old style” source tarball, which is conceptually identical to what it was before, i.e., one does ‘configure’, then ‘make’ and finally ‘make install’. Note that CCP4 Updates cannot be applied to thus compiled CCP4 setups. We distribute the old style tarball for the very last time, considering 6.4.0 Release as transient in this sense b) the “new style” source tarball, which contains both source codes and a system to update compiled setups directly from CCP4 repositories. The “new style” compilation and building is different from the one in “old style” tarballs, but not overly complex. Please see full set of instructions at http://devtools.fg.oisin.rc-harwell.ac.uk/src-readme.html. The updates will be done from the release branch of CCP4 repositories, from which all CCP4 updates are generated. c) CCP4-JHBuild. This is a comprehensive build system, used by CCP4 in-house. It builds the latest, untested, unreleased versions of CCP4 libraries and programs and is intended primarily for CCP4 developers. Instructions are given at http://devtools.fg.oisin.rc-harwell.ac.uk<http://devtools.fg.oisin.rc-harwell.ac.uk/>/. Finally, please note that CCP4 Core Group supports a number of nightly builds on various platforms, which are accessible through CCP4 Developers Page at http://www.ccp4.ac.uk/dev/main.php. 3. ARP/wARP 7.4 co-distribution ARP/wARP Model Building Software is developed in EMBL-Hamburg and is co-distributed with CCP4 starting from Release 6.3.0. Installation of ARP/wARP Software, whether through CCP4 Setup Manager or by downloading a tarball from CCP4 Download Pages, requires academic users to comply with the terms of separate license agreement and provide their names and e-mail addresses for license purposes. Academic licenses are free and granted instantly before download starts. Commercial users are required to purchase their license directly from EMBL-EM and have their reference number ready prior the download. Please note that CCP4 does not deal with ARP/wARP licensing. Note that ARP/wARP may be installed in addition to pre-existing or compiled CCP4 setups from standalone ARP/wARP packages available from either the CCP4 Download Pages or the ARP/wARP web-site at EMBL-Hamburg. ARP/wARP 7.4 includes the following major updates and changes (on behalf of Victor Lamzin): Protein chain tracing: · The use of non-crystallographic symmetry has been further improved, the built protein models are now 5% more complete and the fragments are 50% longer. The NCS order is automatically adjusted. · The accuracy of the estimated model correctness has been improved from 3.0 to 2.5 %. Ligands: · A new algorithm with full conformational search for fitting partial ligands into an electron density (cocktail screening) has been implemented. · Given a specified electron density the most common ligands in the PDB are screened in all conformations. CCP4i GUI: · The ARP/wARP CCP4i interface has been extended to accommodate accumulated developments. ArpNavigator: · The ArpNavigator is now more robust, the default appearance and object rastering have been made nicer. · The "Quick Action"-Menu has been improved and the protocols for ligand building become conveniently accessible. · A new button has been added 'Submit to ViCi' for an in-silico ligand-based drug design. Installation: · The ARP/wARP installer has been modified so that there is no need anymore to source ARP/wARP setup files in .cshrc/bash\_profile. By sourcing the CCP4 setup the settings to source ARP/wARP should be installed automatically. · The supported computer platforms are Mac Intel (10.5 to 10.8) and Linux (both 32 and 64-bit versions). · CCP4 6.4.0 and Refmac 5.7.0032 (or higher) are the recommended versions to use with ARP/wARP 7.4. 4. Changes in binary builds for Mac OSX The CCP4 Core Group has decided to switch from 32-bit to 64-bit Mac OSX builds and drop support for 32-bit architectures. This decision was taken after a survey on the CCP4 BB, which resulted in only a few 32-bit Mac machines in use reported. Such low numbers makes it extremely uneconomical to support 32-bit builds on Mac OSX any longer. During that survey, a confusion was revealed that most of those who reported having 32-bit machines, with very few exceptions, actually had 32-bit Mac OSX installed on 64-bit hardware. Such setups are perfectly capable of running 64-bit codes. However, you are welcome to report 64-bit incompatibility to us in order to let us know the actual number of those who are affected. If you suffer from this change, one possible solution is to compile CCP4 from sources, however, we did not test the procedure for 32-bit Mac architectures. 5. Binary builds for Linux Starting with version 6.3.0, CCP4 began distributing both 32-bit and 64-bit precompiled binaries for Linux. Note that 64-bit codes will not run on 32-bit architectures, and 32-bit codes will run on 64-bit setups only if 32-bit libraries are installed (not a default for most Linuxes). THEREFORE: PLEASE MAKE SURE THAT YOU HAVE SET THE 32-bit/64-bit SWITCH ON TOP OF THE DOWNLOAD PAGES CORRECTLY BEFORE ALL! 6. Binary builds for Windows The Windows build remains 32-bit. Due to the general tendency to larger datasets, some CCP4 components use considerable initial RAM allocations, therefore, a minimum 2GB of RAM is now required. However, some data sets may cause even larger allocations. If you find that your data is likely to require allocations in excess of 4GB of RAM and you are using 64-bit Windows, please contact CCP4 helpdesk, we are testing 64-bit binaries. We would like to thank all of the developers who have contributed into CCP4 6.4.0, 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. CCP4 is supported by the BBSRC UK through grant BB/F0202281, as well as by the number of industrial users. CCP4 6.4.0 is out now, and we hope that you will find it a helpful advance in crystallographic computing. Many thanks for being CCP4 users, CCP4 Core Team -- Scanned by iCritical.
