> 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 [log in to unmask]<mailto:[log in to unmask]>. 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.
>
>
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