Hi there,
I'm keen to get up and running with CC44_7. I have installed and I'm trying to import old projects on my windows 10 machine. Whilst I can allocate a project to the old directory, I can't see any way that ccp4i2 can read and import these projects.
The interface is asking for .ccp4db.zip files which are not present in the project folders. Any suggestions?
Joel
-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Charles Ballard
Sent: Saturday, 6 February 2016 6:19 AM
To: [log in to unmask]
Subject: [ccp4bb] Release of CCP4 7.0.002 on windows
The CCP4 Core Team is pleased to announce the release of CCP4 7.0 on windows x86_64 and i686.
The .exe installer is based CCP4 version 7.0.002, including these updates on top of the base 7.0 release.
*IMPORTANT*
a. If you were one of the fortunate few who downloaded CCP4 7.0 for windows over the past couple of days, can you please reinstall as a couple of important fixes have now been made.
b. Due to possible clashes with earlier items in the Registry it is HIGHLY recommended that older versions of CCP4 on windows be deleted before installation.
c. Coot integration with ccp4i2 on windows
Coot is the integrated molecular graphics tool for model building and refinement with ccp4i2, and efficient use of the system needs coot to be installed and the GUI configured to know its installation location. Coot is installed as a separate download from the CCP4 downloads page
http://www.ccp4.ac.uk/downloads
To configure ccp4i2 so that it can use coot, you should
1) Launch ccp4i2,
2) Open the preferences dialog (ccp4i2 window->"Edit"->"Preferences")
3) Select the "Other Software Tab"
4) In the line "Coot executable file path", either
a) enter the path to the file "runcootwin.bat" in your distribution (e.g.) E:\WinCoot\runwincoot.bat, or
b) click the "folder" icon at the far right of the line to allow you to browse to the location of that file.
5) Click "Apply"
We recommend that you exit ccp4i2 and restart it for the change to take effect.
d. Coot integration with ccp4i on windows
1) Launch ccp4i
2) Open the configure interface window (ccp4i window -> "System Administration" -> "Configure Interface")
3) Set location of Coot executable (default "C:/WinCoot/runwincoot.bat")
4) Click "Save"
5) Relaunch interface
Have fun!
CCP4 Core Team
> 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.
>
> 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
>
> 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.
>
> 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). 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. 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/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] 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
|
