> Does this mean I need to download the installation package from the CCP4
- yes > and is this why the update tool in 6.4.0 is not showing up the latest release? - no, this must be something different > Should I install into the current 6.4.0 directory or a new one? - some CCP4 components rely on CCP4 directory name to be correct. It is therefore advisable to keep it as suggested by CCP4 installer/tarball, which is ‘ccp4-6.5’ for this release > Will my existing data folders etc. be retained? - you should be able to see all your data and projects in ccp4i after upgrade; I do not remember reports on lost data due to CCP4 upgrade from users :) Best regards, Eugene > > Thanks. > Mohamed > > On 18/12/2014 21:54, Eugene Krissinel wrote: >> Dear CCP4 Users, >> >> >> >> The CCP4 Core Group is very pleased to announce the release of the latest >> version of the CCP4 Software Suite. Version 6.5 (Hellifield) is now >> available from the CCP4 download website: >> >> >> >> http://www.ccp4.ac.uk/download.php >> >> >> >> The release is available for Linux, Mac OSX and Windows platforms. This >> release mostly consolidates updates in CCP4 6.4.0 update series, but also >> introduces a number of technical improvements and new features. >> >> >> >> The whys and wherefores: >> >> >> >> Why is it necessary to switch to CCP4 6.5 now? >> >> a) Because it brings new features and updates >> >> b) Because the update line of 6.4.0 is now discontinued >> >> c) Because support for 6.4.0, as well as for all earlier versions of CCP4, >> is now stopped. >> >> >> >> Why did CCP4 make a new release rather than keeping on updating the current >> one? >> >> Because over the last year, the difference between the release and the >> development (trunk) branches of CCP4 has reached a point where merging them >> takes a considerable effort and makes updates unfeasible. >> >> >> >> Why 6.5 and not 6.5.0? >> >> Because the last numeral will be now defined by the last CCP4 update applied >> (not to worry, updates will not change the CCP4 directory name, which will >> remain ‘ccp4-6.5’ for the lifetime of the release). The full version number >> (including updates) will be printed on top of all the log files. >> >> >> >> >> >> 1. New Components and Updates >> >> >> >> Below is a selected list of updates and new components; for more details >> please see the individual program documentation. >> >> >> >> New: >> >> >> >> Privateer-validate: validation of carbohydrate structures from Jon Agirre >> (The University of York) >> >> - Calculates the conformation of pyranoses and furanoses using the >> Cremer-Pople algorithm. >> >> - Compares the detected conformation to the minimal-energy conformation of >> the sugar. >> >> - Performs basic stereochemistry and geometry checks. >> >> - Computes a real space correlation coefficient against a positive omit >> density. Outputs 2mFo-DFc, mFo-DFc and omit mFo-DFc maps. >> >> - Describes N- and O-glycan structures. >> >> >> >> Feckless: combination of multilattice files from Mosflm for Pointless & >> Aimless, from Phil Evans (MRC/LMB). >> >> >> >> Acedrg v90 and LibG: chemoinformatics support for Refmac (geometry and >> restraint generator), from Garib Murshudov’s team at MRC/LMB. >> >> >> >> Blend v0.5.10: optimum selection of multi-crystal datasets for merging from >> James Foadi, MPL, Harwell, UK >> >> - suggests favourable or desirable combinations of datasets >> >> - provides tools for easy management of multi-crystal operations >> >> - reads in integrated data from MOSFLM or XDS >> >> - outputs scaled data and associated statistics using POINTLESS and AIMLESS >> >> >> >> Crank-2: conceptually redesigned and considerably improved Crank pipeline >> for automatic experimental phasing from Navraj Pannu and Pavol Skubak, >> University of Leiden, The Netherlands. >> >> >> >> >> >> Updated: >> >> >> >> Aimless v0.5.1 (Scaling multiple observations of reflections) >> >> - some options for XFEL data (SAMPLESD, Rsplit, batch rejection) >> >> - use estimated scale parameter errors in sigma(I); improved SDcorrection >> >> - CC(1/2) maximum resolution from curve fit >> >> - matrix of run-run correlations >> >> >> >> Pointless v1.9.23 (Laue group determination) >> >> - bug fixes >> >> >> >> Prosmart v0.845 (Macromolecular restraints generator) >> >> - Enabled structural comparison and restraint generation functionalities >> with DNA/RNA chains >> >> - Ability to calculate and display screw axis-angle representation >> corresponding to rigid-body transformations >> >> - Support for UCSF Chimera >> >> - Various technical enhancements and changes to default >> parameters/behaviour >> >> >> >> Buccaneer v1.6.0 (Model autobuilding) >> >> - new modes for building after molecular replacement, with facilities for >> differing levels of data quality and model agreement >> >> >> >> CCP4 MG v2.10.0 (Molecular graphics) >> >> - Visualization of multiple bonds and aromatic rings >> >> - Load molecules from SMILES string >> >> - Load molecules from ccp4srs database >> >> - Better hydrogen bond calculation parameters and base pair sticks >> >> - Many bug fixes. >> >> >> >> Xia2 v0.3.8.0 (Automated data processing) >> >> - Added support for DIALS software >> >> - Create AIMLESS xml output >> >> - Bug fixes >> >> >> >> ccp4um v1.24 (CCP4 Update Manager) >> >> - Allows off-line updating without connection to X11 >> >> >> >> >> >> Refmac v5.8.0103 (Macromolecular refinement) >> >> >> >> CTruncate v1.16.5 (Intensity to amplitude conversion and reflection data >> statistics) >> >> >> >> Superpose v1.0.4 (Macromolecular structure superposition) >> >> >> >> Coot v0.8.1 (Interactive model building) >> >> >> >> ARP/wARP v7.5 (Model building suite from EMBL-Hamburg) >> >> >> >> MrBUMP (Phmmer, which is included in the suite, is now used for >> sequence-based searching) >> >> >> >> AMPLE (Supports use of QUARK generated decoys for use in molecular >> replacement) >> >> >> >> CCP4 Graphical User Interface: >> >> - Incremental changes to accommodate new program and program updates >> >> >> >> >> >> 2. Technical notes >> >> >> >> In release 6.5, there are many changes in CCP4 the repositories and the >> build system. You may also find rearrangement of certain files in CCP4 >> setups. The most important changes are listed below. >> >> >> >> 2.1 Coot is fused with the CCP4 core on Linux and Mac OSX, and may be >> invoked as $CCP4/bin/coot. Mac OSX distribution still has “Coot application” >> in $CCP4/coot.app, which may be used as usual, e.g., started by >> double-clicking in Finder. On Windows, we still provide WinCoot as a >> standalone package from Bernhard Lohkamp (Karolinska Institute, Sweden). >> >> >> >> 2.2 CCP4 MG is, like Coot, fused with the CCP4 core on all systems, and may >> be invoked as $CCP4/bin/ccp4mg on Mac OSX and Linux, or simply ccp4mg on >> Windows. The Mac OSX distribution still has “QtMG application” in >> $CCP4/QtMG.app, which may be used as usual, e.g., started by double-clicking >> in Finder. >> >> >> >> 2.3 CCP4 Update manager, ccp4um, is modified such that it does not need >> connection to run X11 in offline mode. This should help system >> administrators to automatically update CCP4 setups using a remote cron. The >> corresponding command is ‘ccp4um -auto’. >> >> >> >> 2.4 Source code distribution 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 tarballs, used in CCP4 releases up to 6.4.0 >> (where one unpacks and then does ‘configure’, then ‘make’ and finally ‘make >> install’), are now completely retired. >> >> b) The only way to build CCP4 from sources is now described in detail here: >> http://devtools.fg.oisin.rc-harwell.ac.uk/src-readme.html. The new system is >> solely based on CCP4 JHBuild (http://devtools.fg.oisin.rc-harwell.ac.uk/), >> but has 2 variants, one with downloading source codes as a tarball prior to >> building, and another one – with simultaneous download and building. Please >> find more details in first reference above. >> >> >> >> Finally, please note that the 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 co-distribution >> >> >> >> CCP4 is proud of maintaining the joint distribution with the ARP/wARP Model >> Building Software, developed in EMBL-Hamburg. The first CCP4 – ARP/wARP >> joint release took place with CCP4 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 a >> separate licence agreement and to provide their names and e-mail addresses >> for licence purposes. Academic licences are free and granted instantly >> before download starts. Commercial users are required to purchase their >> licence directly from EMBL-EM and have their reference number ready prior >> the download. Please note that CCP4 does not deal with ARP/wARP licencing >> and does not keep account of user data submitted through CCP4 web pages or >> Setup Manager for obtaining ARP/wARP licence. Use of ARP/wARP Software >> should be acknowledged separately from CCP4, using appropriate references >> from ARP/wARP web-site. >> >> >> >> ARP/wARP 7.5 includes the following major updates and changes (on behalf of >> Victor Lamzin, EMBL-Hamburg): >> >> >> >> Increased performance of protein model building through: >> >> - improved polypeptide recognition, >> >> - NCS-restraints, >> >> - atom update, >> >> - SAD-refinement option, >> >> - estimation of solvent content >> >> - and model accuracy >> >> >> Improved stability of beta-strand, DNA/RNA and solvent building >> >> >> >> “Fit Ligand” incorporates 84 most common ligands now and >> >> >> >> uses cif files defining bond, torsion and plane restraints >> >> >> >> Incremental improvements in auto-depth view and menus of ArpNavigator >> >> >> >> >> >> >> >> 4. 64-bit and 32-bit bundles >> >> >> >> For the first time, CCP4 offers 64-bit binary distributions for Windows. All >> Windows users running 64-bit versions are encouraged to use these: in rare >> instances, some CCP4 programs may require 64-bit RAM space. The same >> consideration holds for the choice of Linux packages; CCP4 has abandoned >> 32-bit builds for Mac OSX from 6.4.0 series last year. For Linux OSes, >> please note that although 32-bit codes will run on 64-bit setups if 32-bit >> libraries are installed, we strongly suggest our users to use 64-bit builds >> whenever possible. >> >> >> >> You will find 32/64 bit switch in our download pages, on top of download >> links. >> >> >> >> PLEASE MAKE SURE THAT YOU HAVE SET THE 32-bit/64-bit SWITCH CORRECTLY! >> >> >> >> >> >> >> >> Acknowledgements >> >> >> >> We would like to thank all of the developers who have contributed into CCP4 >> 6.5, 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/L007037, as well as by >> the number of industrial users. >> >> >> >> >> >> >> >> Last remarks >> >> >> >> CCP4 6.5 is out now. Although we think of it as our best ever release, most >> certainly, we have overlooked some bugs or inadvertently made mistakes here >> and there. CCP4 is quite a large software suite, and difficult to test >> comprehensively. When bugs and errors are discovered, the best way to deal >> with them is to report straight to us at >> [email protected]<mailto:[email protected]>. We value feedback of our users >> extremely high, 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 Team: >> >> >> >> Marcin Wojdyr >> >> Charles Ballard >> >> Andrey Lebedev >> >> Ville Uski >> >> Ronan Keegan >> >> David Waterman. > >
