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Dear David, If you wish to use the SHELX programs - they are used by several pipelines in ccp4i2 - you should complete the SHELX registration, which has been kept as simple as possible. You will then automatically receive an email to tell you how to download SHELX. The programs shelxc, shelxd, shelxe and anode also come with CCP4 7.0 and its updates, so you may ignore the downloading information unless you wish to use the other SHELX programs, which are primarily intended for small molecules. The SHELX license will not be required to use SHELX via the 'CCP4 onlline' server. Users are encouraged to send questions about SHELX to CCP4BB, and many already do so. I try to respond to them, but sometimes Eleanor is quicker. SHELX does not have its own mailing list but the SHELX homepage provides extensive documentation; this was one reason for making CCP4 7.0 users aware of it. Best wishes, George On 01/08/2016 09:06 PM, David Schuller wrote: > When I installed 7.0 on my workstation, the installation process > automatically sent my browser to the SHELX license web page. Do I need > to do something there? Download something or at least fill in the > license? Or is it all taken care of as part of the CCP4v7 > installation? In which case, why hijack my browser? > > Cheers, > > On 01/07/16 13:07, 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 7.0 (Gargrove) is >> now available from the CCP4 download website: >> >> http://www.ccp4.ac.uk/download.php >> >> At present, the release is available for Linux and Mac OSX platforms. >> We're working hard on making the MS Windows version and it will be >> made available as soon as possible. >> >> The whys and wherefores: >> >> /Why is it 7.0 and not 6.6?/ >> >> Because this release brings a number of new essential components and >> features. They boost CCP4 functionality and give it a new >> look-and-feel far beyond the extent of routine incremental changes. >> Full details are given in the next section. >> >> /Is it really necessary to switch to CCP4 6.5 now?/ >> >> While CCP4 6.5 can be kept on your computers for as long as necessary >> and in parallel to CCP4 7.0, we encourage all our users to switch >> over at first convenience because: >> >> a)all new components and features are essential >> >> b)the update line for CCP4 6.5 is now discontinued >> >> c)support for CCP4 6.5, as well as for all earlier versions of CCP4, >> is no longer available >> >> *1. CCP4 7.0 Release Highlights* >> >> Below is a list of the new and essential additions to the Suite, >> which make this release worthy of inagurating a new version of CCP4. >> >> */SHELX/* >> >> CCP4 is proud to announce its collaboration with Prof. George >> Sheldrick, who has kindly offered his famous SHELX Software for >> inclusion in CCP4. All CCP4 users can now benefit from the >> convenience of a joint installation and maintenance of the SHELX >> Suite, which enhances greatly the Experimental Phasing functionality >> in CCP4. >> >> From George Sheldrick, University of Goettingen, Germany: >> >> “The programs SHELXC, SHELXD, SHELXE and ANODE are included in CCP4 >> starting with CCP4 7.0, and are also used by several pipelines in >> CCP4i2 and CCP4 online. A SHELX licence is still required if these >> programs are obtained as part of a CCP4 installation or update, and >> can easily be generated via the SHELX homepage, but no SHELX licence >> is needed to use the programs from CCP4 online. The licence is free >> for academic use and there are already more than 11000 licensed >> users. The SHELX programs are stand-alone executables with /ZERO >> dependencies/, but currently only SHELXD and ANODE are /highly >> parallel/. The SHELX homepage also provides extensive links and >> tutorials. These programs are suitable for quick routine experimental >> phasing (SHELXC/D/E), for improving models from molecular replacement >> (SHELXE) and for detecting anomalous scattering atoms in refined >> structures (ANODE), However SHELXE, but not the other programs, >> currently requires data to about 2.5A resolution or higher. CCP4i2 >> also facilitates the use of SHELXC/D with CRANK2 and PHASER-EP for >> more demanding problems.” >> >> *CCP4 Interface Version 2 (CCP4i2)* >> >> CCP4 is proud to present the new graphical interface created by the >> team of developers from the University of York and Newcastle >> University, UK, lead by Prof. Martin Noble. The interface has a >> number of new features and an attractive design, making >> crystallographic computations in CCP4 easier than ever. >> >> From Prof. Martin Noble, Newcastle University: >> >> “This release includes the first generally available version of the >> new user interface, CCP4i2. This provides a simplified interface and >> greater automation through the key stages of data reduction, >> structure solution by MR and SAD, refinement and ligand fitting and >> integrates Coot for model building. The results are presented in >> simplified, very graphical reports and all activities are recorded in >> a database. The application is still under very active development >> and users can expect to see new functionality and improved usability >> in forthcoming updates and they are encouraged to contribute and help >> determine priorities with their feedback. First time users are >> recommended to watch either the introductory video >> https://www.youtube.com/watch?v=fB7BRVzBURg or follow the Quickstart >> tutorial.” >> >> CCP4 7.0 retains the previous interface, ccp4i. This is done for >> legacy reasons and for making the transition to ccp4i2 more gradual >> and convenient. Some new packages such as the new advanced EP >> functionality are only available through ccp4i2. Most of the original >> applications have been ported to the new interface but some have yet >> to migrate, so ccp4i may still be required for some users. It should >> be realised, however, that ccp4i will be phased out in future. >> >> *//* >> >> */DIALS/* >> >> The new data processing software “DIALS” is included in CCP4 7.0 >> marking its inaugural appearance in the suite. The Project is a >> collaborative endeavour to develop a new diffraction integration >> software package to meet the data analysis requirements presented by >> recent advances in experimental techniques. >> >> From Gwyndaf Evans, Diamond Light Source, UK: >> >> “DIALS (Diffraction Integration for Advanced Light Sources) is a >> software package for the analysis of crystal diffraction data from >> area detectors. It encompasses all the key steps in analysis from >> the reading of images and spot finding, through indexing, parameter >> refinement and integration. It outputs an MTZ suitable for input into >> POINTLESS and AIMLESS. >> >> In contrast to other integration programs DIALS takes a global view >> of a diffraction data set and can refine crystal and experimental >> parameters for the whole data set prior to integration. DIALS is >> capable of parallel processing using multiple processors and is >> optimised for data measured from Pixel Array Detectors although >> analysis of data from other detectors types is possible. >> >> DIALS is executable from the command line or through scripts. A GUI >> is under development. Running DIALS through Xia2 is the easiest way >> to run the software. >> >> The DIALS license makes it free for use by academics and commercial >> organisations. DIALS is also a development toolkit and users wishing >> to contribute to its development are welcome to do so.” >> >> *ARCIMBOLDO* >> >> Thanks to Dr. Isabel Uson and her team of developers in Barelona the >> ARCIMBOLDO package is now distributed with CCP4. This was made >> possible also by the inclusion of SHELX. >> >> From Dr. Isabel Uson, Molecular Biology Institute of Barcelona, Spain: >> >> “The programs ARCIMBOLDO_LITE, ARCIMBOLDO_BORGES and >> ARCIMBOLDO_SHREDDER are included in CCP4 starting with CCP4 7.0. They >> can be used to phase structures at 2Å or better with helices, >> libraries of small folds and distant homologs, respectively. The >> executables may run both on a multicore workstation, or on a local or >> remote grid. Currently, they are available through the ccp4i >> interface. For additional documentation or reporting problems can be >> found under http://chango.ibmb.csic.es/contact. >> >> We are grateful for feedback!” >> >> *2. Updated CCP4 components* >> >> Below is a selected list of updated components with the summary of >> new features; for more details please see the individual program >> documentation. >> >> *PHASER 2.6.1 *(From Prof. Randy Reed, Cambridge, UK): >> >> ·Molecular replacement calculations now use intensities in preference >> to amplitudes, based on a new treatment of the effect of intensity >> measurement errors >> >> ·Improved handling of weak data when normalising, correcting for >> anisotropy and characterising translational non-crystallographic >> symmetry (tNCS) >> >> ·Models with high TFZ score that fail packing tests are automatically >> pruned using a local occupancy refinement protocol >> >> ·Subgroups of space groups are listed and, if twinning is suspected, >> molecular replacement can be carried out in a subgroup >> >> ·Phased translation function can be used, even as part of the MR_AUTO >> search >> >> ·The magnification factor for a cryoEM reconstruction used as a model >> can be refined >> >> ·SAD likelihood is reported as a log-likelihood-gain score giving the >> improvement over a null hypothesis >> >> ·In tNCS characterisation, the Patterson is analysed to suggest an >> appropriate NMOL parameter indicating the number of copies related by >> successive applications of NCS translations. >> >> *Pointless 1.10.18 *(From Prof. Phil Evans, MRC/LMB, Cambridge, UK) >> >> ·Improved resolution cutoff for scoring >> >> ·XML additions for ccp4i2. >> >> ·Added explicit RUN definition >> >> ·Many bug fixes, including in C2 <-> I2 conversions >> >> *Aimless 0.5.21*(From Prof. Phil Evans, MRC/LMB, Cambridge, UK) >> >> ·XML additions for ccp4i2 >> >> ·More robust handling of very low multiplicity data >> >> ·Add printing of resolution estimate at I/sd > 2 as well as > 1.5 >> >> ·More robust SD correction >> >> ·Many bug fixes. >> >> *COOT 0.8.2 *(From Dr. Paul Emsley, MRC/LMB, Cambridge, UK): >> >> New features: >> >> ·Add dictionary-based atom name matching in pyrogen >> >> ·Add ligand fragment flipping >> >> ·SMILES drag and drop added to LBG >> >> ·Use pyrogen by default if mogul available >> >> ·Surface points are now exported from HOLE. >> >> ·Clicking on a Het-group now reports the name in the status bar >> >> ·Added function map-statistics to return map statistics >> >> Changes: >> >> ·EDS Resolution added to PDB Validation dialog >> >> ·The Residue numbers are reported in the refinement dialog when >> creating a cis-peptide >> >> ·Ligands in Rainbow mode are no longer blue >> >> ·Colour-by-chain now shows disulphide bonds >> >> ·Refinement drag elasticity increased >> >> ·Global translations towards the molecule centre removed on model >> morphing >> >> Bug fixes: >> >> ·Improvement in PDB->SHELXL ins output >> >> ·Fix problem of deleting all atoms in Baton Build atoms molecule >> >> ·The NCS master chain in Copy NCS Residue Range now works >> >> ·"Clear Latest Distance" crashes coot >> >> ·Fix output format of external restraints >> >> ·Torsion-based ligand fitting improvements >> >> ·A model with hydrogen atoms displayed in CA+Ligands mode used to >> show the hydrogen atoms even if hydrogen atom were off >> >> ·Fix occasional graph data range anomaly >> >> ·Add missing plane distortions in print_residue_distortions() >> >> ·PISA interface works with newer version of Pisa >> >> ·Only check once for probe when showing the Validation menu. >> >> ·Resetting of Own font colour on opening the preferences dialog fixed. >> >> *BLEND 0.6.18*(Optimum selection of multi-crystal datasets for >> merging, from James Foadi, MPL, Harwell, UK) >> >> ·New "annotated dendrograms" (with merging statistics and aLCV >> values) can now be produced running blend in the new "graphics" mode. >> >> ·New "F" (filtering) and "P" (pruning) variants have been added to >> combination mode to enable automated elimination of whole datasets >> and/or parts of them >> >> *Xia2 **0.4.0.0*(From Graeme Winter, Diamond Light Source, UK) >> >> ·Full support for processing with DIALS / Aimless >> >> ·Proper support for small molecule crystallography >> >> ·Enhanced support for multi-axis goniometry >> >> ·DIALS / Aimless now default processing pipeline** >> >> ** >> >> *Buccaneer 1.6.1*(Automatic model building, from Kevin Cowtan, >> University of York, UK) >> >> ·Automatic sequencing and pruning of chain ends to match the expected >> sequence >> >> ·Option for automatic preservation of existing non-protein features >> (currently command-line only) >> >> *Privateer-validate*(Validation of carbohydrate structures,from Jon >> Agirre and Kevin Cowtan, University of York, UK) >> >> ·Generation of monoperiodic torsion restraints for keeping the >> minimal-energy conformation during real and reciprocal space refinement. >> >> ·Enabled validation of novel modified sugars also through CCP4i2. >> >> *Crank-2*(Automatic experimental phasing from Navraj Pannu and Pavol >> Skubak, University of Leiden, The Netherlands) >> >> ·A new SHELX pipeline (available in ccp4i2 only) >> >> ·SIRAS and MAD in Crank2 (available in ccp4i2 only) >> >> ·Improved MR-SAD in Crank2 >> >> *CCP4 MG 2.10.5*(From Stuart McNicholas and Liz Potterton, University >> of York, UK) >> >> ·Glycoblocks cartoon representation of sugars. >> >> ·Introduced experimental interface to model preparation stages of MrBUMP. >> >> ·Simple neighbourhood of ligands menu selections and other >> assignment/selection and picture wizard improvements. >> >> ·Better object movement behaviour. >> >> ·Many memory leaks fixed. >> >> ·ccp4i2 integration. >> >> *Prosmart v0.85*(Comparative structural analysis and restraint >> generation, from Robert Nicholls, MRC/LMB, Cambridge, UK) >> >> ·Restraint filtering based on B-factor distributions >> >> ·Hybrid-36 PDB format support for 2-letter chain IDs >> >> ·H-bond restraints for waters >> >> *Gesamt 1.09*(General structure aligner and superposer, from Eugene >> Krissinel, CCP4, UK) >> >> ·Multiple structural alignment >> >> ·Fast structural screening of the PDB (requires a local copy of the PDB) >> >> *QtPISA 2.06*(Protein interfaces and assemblies explorer, from Eugene >> Krissinel, CCP4, UK) >> >> ·Stock-based analysis of protein oligomeric states >> >> *AMPLE*(Ab-initio modelling for molecular replacement, from Prof. Dan >> Rigden and Jens Thomas, University of Liverpool, and Ronan Keegan, CCP4) >> >> ·Improved handling of side-chains with QUARK models. >> >> ·Ability to use idealized helices as MR search models >> >> ·New output presentation interface making it easier to access results >> >> ·Restart capability added >> >> ·Improved logging and output to facilitate user bug reports >> >> ·Bug fixes. >> >> *3. ARP/wARP co-distribution* >> >> Since CCP4 Release series 6.3.0, CCP4 and ARP/wARP team at >> EMBL-Hamburg, Germany, maintain the joint distribution of the >> ARP/wARP Model Building Software. 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 license does not cover the use of ARP/wARP and that CCP4 does >> not keep an 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. >> >> From Victor Lamzin, EMBL-Hamburg, Germany: >> >> *ARP/wARP 7.6 *provides improved performance in protein chain >> tracing, particularly at resolution below 2.5 A, as well as in >> DNA/RNA fragment building. >> >> Specifically: >> >> Protein model building >> >> - Dipeptide conformational space is introduced for the selection of >> the chain path >> >> - NCS restraints are now default at resolution 1.5 A or lower >> >> - Side chain fit is improved with additional real-space refinement >> >> - Check for java is introduced and the use of conditional restraints >> is turned off if java is not installed (can occur on OSX 10.10 and >> 10.11). >> >> DNA/RNA building >> >> - The tracing of the nucleotide chain tracing is enhanced with the >> addition of the second algorithm for phosphate detection >> >> - Chain tracing now proceeds in 5-cycle iterative manner, as for the >> protein chain tracing >> >> Solvent building >> >> - Default density thresholds for atom update are optimised >> >> Other changes >> >> - ARP/wARP installer is made more robust >> >> *4. Technical notes* >> >> For Mac OSX and Linux platforms, on-line setup through CCP4 Setup >> Manager is the recommended option. Currently, this is the only option >> available, but we will provide off-line distros for users with >> restrictive network setups, soon after. >> >> Please pay attention to the distinction between 32-bit and 64-bit >> bundles and choose the one suitable for your OS. Support for 32-bit >> Mac OSX has been discontinued since CCP4 6.3 and the 64-bit version >> is the only available option now. For Linux OSes please note that, >> 32-bit codes will run on 64-bit systems if 32-bit libraries are >> installed. However, we strongly recommend that users use 64-bit >> builds whenever possible. You will find a 32/64-bit switch on our >> download pages, just above the download links. >> >> Finally, please note that the CCP4 Core Group supports a number of >> nightly builds on various platforms, which are accessible through the >> CCP4 Developers Page at http://www.ccp4.ac.uk/dev/main.php. >> >> *5. CCP4 online* >> >> CCP4 users can now access selected CCP4 applications as web-servers >> through out CCP4 on-line server >> (<http://www.ccp4.ac.uk/ccp4online>http://www.ccp4.ac.uk/ccp4online). >> Services include: >> >> ·Balbes molecular replacement pipeline >> >> ·MrBUMP molecular replacement pipeline >> >> ·Zanuda space group and crystallographic origin validation >> >> ·PISA interface and oligomeric state analysis >> >> In the near future, the experimental phasing pipelines Crank-2 and >> SHELX will be added to the list along with AMPLE, the ab initio >> modelling for MR pipeline. Using CCP4 on-line is beneficial where >> sufficient computational resources and bioinformatics support are not >> available locally. It also exploits a parallel cluster backend >> allowing for quicker results, especially where the MR pipelines are used. >> >> *Acknowledgements* >> >> We would like to thank all of the developers who have contributed to >> CCP4 7.0, 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. Vaginand 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/L007037, as well as by our industrial users. >> >> *Last remarks* >> >> CCP4 7.0 is out now. It initiates a whole new version of the suite >> with updates and further releases to come in the following years. 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 [log in to unmask] >> <mailto:[log in to unmask]>. 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 >> >> Marcin Wojdyr >> >> Karen McIntyre >> > > > -- > ======================================================================= > All Things Serve the Beam > ======================================================================= > David J. Schuller > modern man in a post-modern world > MacCHESS, Cornell University > [log in to unmask] -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-33021 or -33068 Fax. +49-551-39-22582