Not yet all. It is a significant project, but one that is very much underway. -- David
On Thu, 23 Apr 2020 at 18:55, David Schuller <schul...@cornell.edu> wrote: > Coincidentally, Python 2 had its final release just a few days ago. I > trust python components of CCP4 are all now using Python 3. > > https://www.theregister.co.uk/2020/04/21/the_final_python_2_release/ > > - > ======================================================================= > All Things Serve the Beam > ======================================================================= > David J. Schuller > modern man in a post-modern world > MacCHESS, Cornell University > schul...@cornell.edu > > ------ > > > On 2020-04-23 12:30, 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 7.1 (Skipton) is now available > from the CCP4 download website <http://www.ccp4.ac.uk/download.php>. The > release is available for all MS Windows, Linux and Mac OSX platforms. > Is it really necessary to switch to CCP4 7.1 now? > > While CCP4 7.0 can be kept on your computers for as long as necessary and > in parallel to CCP4 7.1 (Mac OSX and Linux only), we encourage all our > users to switch over at first convenience because: > > 1. the release brings new, updated and improved components that make > structure solution with CCP4 yet more efficient and easy > 2. the update line for CCP4 7.0 is now discontinued > 3. support for CCP4 7.0, as well as for all earlier versions of CCP4, > is no longer available > > CCP4 7.1 Release Highlights > > CCP4 Release 7.1 comes as a complete modernisation of version 7.0, which > have seen the longest life time ever in CCP4 history, being released more > than 4 years ago and complemented with 79 updates. However, changes in > operating systems and advances in computer languages, accumulated over this > significant time period, have made it necessary to introduce technical > modifications, such as progressing to C++-11, that could not be carried out > using the CCP4 update system. > Main Updates and Improvements > > CCP4 7.1 represents the final state of 7.0 update series, complemented > with newest versions of many important components, for example: > COOT 0.9 > > *The latest version of Interactive Model Building Software from Dr. Paul > Emsley, MRC/LMB, Cambridge, with many improvements and new features.* > > Currently available only for Mac OSX and Linux users. The corresponding > update for Windows systems will be issued as soon as feasible > DIALS 2.1 > > *Diffraction image processing software from Diamond Light Source Ltd., > CCP4 and the Lawrence Berkeley National Laboratory. DIALS now includes a > scaling module and improved multi-crystal symmetry tools.* > DUI 2019.12 > > *A Graphical User Interface for DIALS programs.* > XIA2 0.6.0 > > *Automated diffraction image processing using an expert system.* > PHASER 2.8.3 > > *Maximum likelihood structure solution software from the group of Prof. > Randy Read, Cambridge.* > SHELX > > *SHELX Software from Prof. George Sheldrick, University of Goettingen, > Germany (SHELXE is supported by Dr. Isabel Uson, Barcelona, Spain)* > Buccaneer > > *BUCCANEER Software from Dr. Kevin Cowtan, University of York, UK, with > important fixes and improvements* > > and many others. CCP4 continues to provide > ARP/wARP 8.0 > > *Automated Model Building Software from Dr. Victor Lamzin, EMBL Outstation > in Hamburg, Germany* integrated with the CCP4 Core package. > > In CCP4 7.1, you will find considerably advanced and improved: > CCP4i2 > > *CCP4 Graphical Interface with many tasks and report pages revised and > partly redesigned, numerous bugs fixed and overall stability enhanced.* In > particular, CCP4i2 now contains the deposition module, which allows you to > prepare files in mmCIF format, suitable for deposition to the PDB in a > fairly automated manner. > New Software > > In addition to numerous modifications, advances and updates, CCP4 7.1 > introduces a few brand new components: > GEMMI > > *C++/Python application and library for handling coordinate and reflection > data (from Marcin Wojdyr, Global Phasing Ltd., Cambridge, UK)* > > GEMMI is a highly efficient and sophisticated package for manipulating > coordinate and reflection data in various formats (such as .pdb, .mmcif, > .mtz). The package is very useful for developing MX-related applications in > C++ and Python. > MRparse > > *Assistant application for making and analysing search models for > Molecular Replacement (from the group of Prof. Daniel Rigden, University of > Liverpool, UK)* > > MRparse finds suitable structure homologs, aligns and represents them > graphically for reference and more efficient MR ensembling. Available in > CCP4i2 interface. > CCP4 Cloud > > *A framework for distributed CCP4 Computation* > > CCP4 Cloud represents a conceptually new approach to organising and > maintaining crystallographic projects in CCP4 and running CCP4 tasks. With > this system, you can keep all your data and projects in the Cloud and > manage them using any modern browser running on a desktop PC, laptop, > tablet/ipad or even a smartphone, from any geographic location. In CCP4 > Cloud, only the initial data need to be uploaded once; within a Project, > the data is passed from task to task behind the scenes, without exchange > with the client device. CCP4 Cloud represents Projects as branched trees, > making the structure solution pathway perfectly transparent and easily > reconcilable. All main stages of structure solution in MX: image > processing, phasing, model building, refinement, validation and PDB > deposition are presented in CCP4 Cloud as a collection of more than 75 > tasks. Interactive tasks, such as Coot, are also available in CCP4 Cloud. > Using such tasks requires a local CCP4 7.1 setup, which contains the CCP4 > Cloud Client, a piece of software linking CCP4 Cloud with Coot installed > locally. Just double-click on the CCP4 Cloud Client icon (CCP4 Diamond with > a cloud and wireless sign) in order to start using CCP4 Cloud right after > installation of CCP4 7.1 (you will be required to register as CCP4 Cloud > user first time). > > The CCP4 Core Group will be happy to help anyone to start using CCP4 > Cloud. Development of CCP4 Cloud was supported by BBSRC UK Grant > BB/L007037/1 and is a result of a collaborative effort of many developers > and enthusiasts. > CCP4build > > *Automated model builder (from Eugene Krissinel and Andrey Lebedev, CCP4 > Core Group)* > > CCP4build combines several applications: CParrot, CBuccaneer, Refmac, Coot > and EDStats, for the enhancement of automatic model building in CCP4. > CCP4build explores several model building scenarios in an iterative > approach with rollbacks, and adjusts automatically to building in both > experimental phases and phases obtained in the course of molecular > replacement. CCP4build is available in CCP4 Cloud. > BUSTER interface > > *Interface to BUSTER software from Global Phasing Ltd.* > > The interface allows a user to refine macromolecular structures with > BUSTER software from Global Phasing Ltd. The interface is available through > the CCP4 Cloud - both in your own installation as well as through the CCP4 > Cloud service at RC Harwell (UK). > > The latter case requires online authorisation for academic users with > Global Phasing Ltd. (which are kindly providing the software to all > academic users free of charge), which is done via an authorisation facility > found in user’s account settings. Use of the interface within your local > CCP4 Cloud installation requires a separate, local installation from > www.globalphasing.com. > Technical notes > > For Mac OSX and Linux platforms, on-line setup through the CCP4 Setup > Manager is the recommended option. CCP4 Setup Manager enables you to choose > a desirable set of components, download, install and configure them > automatically. > > Before installing CCP4 7.1, PLEASE MAKE SURE THAT NO CCP4 PROGRAMS ARE > RUNNING, PARTICULARLY CCP4i AND CCP4i2. The simplest way to achieve that is > to REBOOT YOUR COMPUTER BEFORE THE INSTALLATION OF CCP4. > > Installation on MS Windows systems requires downloading the whole package > as an executable installer and running it on your machine. Be prepared to > see a warning message from MS Windows, suggesting that the software may be > harmful for your system – please trust CCP4 and choose “install anyway”. It > is necessary that you REBOOT YOUR WINDOWS PC AFTER INSTALLATION, before > attempting to run any of CCP4 programs. > > We advise you to always include Coot in your installation package and > install it simultaneously with the rest of CCP4. If you intend to use Coot > from other sources, be prepared to link it with CCP4 after installation and > manage it separately. CCP4 cannot provide updates to Software installed > from sources other than CCP4 and cannot guarantee a flawless integration of > such software – although we will do our best in order to resolve any issues > you may encounter. > > Please note that, starting from CCP4 7.1, 32-bit packages are no longer > available. > Acknowledgements > > We would like to thank all of the developers who have contributed to CCP4 > 7.1, 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. > > 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/S006974/1 (CCP4 Advanced Integrated Approaches to Macromolecular > Structure Determination), as well as by our industrial users. > Final remarks > > CCP4 7.1 is out now. 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 c...@stfc.ac.uk. 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 > Oleg Kovalevskiy > Tarik Drevon > Karen McIntyre > > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > > - > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
