| Contact info | CCP4 projects | Software | Programming | Downloads | PX links | Pictures | Background | Non-CCP4 |
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I'm Peter Briggs,a scientific programmer with the CCP4 project based within the Computational Science and Engineering Department at STFC Daresbury Laboratory.
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Dr Peter J Briggs
CCP4 Computational Science and Engineering Department STFC Daresbury Laboratory Daresbury Warrington WA4 4AD UK tel:+44 1925 603826 fax:+44 1925 603825 E-mail: p.j.briggs@dl.ac.uk |
I am the CCP4i Project Coordinator. Some current projects:
An updated interface to Phil Evans' program POINTLESS:
This is a prototype intended to address the new features in the latest versions of POINTLESS for handling multiple input file. (24/10/2007)
Proposals to reorganise
the CCP4i modules (4/5/2006)
Outline of the technical changes required:
Changes to the CCP4i
Modules & Tasklist Presentation (21/12/2006)
Proposed CCP4i Plugins: notes on possible ways to launch external applications from within CCP4i (22/12/2006)
Some less recent developments and links:
An interface for running the SHELXC, D and E programs is now in the official release of CCP4 6.0. Related materials:
Some other relevant general links:
CCP4i Main Page
at DL
This includes links to Tcl/Tk and BLT resources
CCP4i Projects Page
Some general developments
CCP4i Developer's Resources can now be found on the official Developers Page
CCP4 is a partner in the EU Framework 6 Integrated Project "BIOXHIT", more details of the project and the CCP4 contribution can be found here:
There are some related documents here:
Some software that I've developed while working for CCP4:
smartie is a set of Python classes and methods for parsing CCP4 logfiles. At the moment it is geared towards extracting lists of programs from CCP4i logfiles, but it also has useful classes for handling and interrogating loggraph-formatted tables. Smartie has been used for a while now in the MrBUMP automated molecular replacement pipeline.
The current version is 0.0.13 and be downloaded here:
You can also see the documentation, and read the CCP4 newsletter article about smartie.
baubles is an experimental CCP4 logfile reformatter built on top of smartie, which has been developed in collaboration with Kevin Cowtan and Phil Evans. You can see some examples of reformatted logfiles and download the latest version if you are interested in using baubles.
A conversion utility to generate CIF from MTZ files. This is intended to replace the OUTPUT CIF option of MTZ2VARIOUS, and is able to output multiple datasets in a single CIF.
MTZ2CIF will be in the next major release of the CCP4 suite (nominally 6.1), otherwise you can download and install from source code here:
You can also see the documentation for MTZ2CIF.
A utility which allows interrogation of the CCP4 symmetry library, and manipulations of symmetry operator representations.
It provides a way to look up spacegroup information and to acquire data about symmetry operations expressed in different formats, for example as matrices or as strings of the form "X+1/2, Y+1/2, Z". It also provides a way of converting between these different formats.
The documentation for SYMCONV gives more details of the features of the program. SYMCONV will be released as part of CCP4 6.1.
MapSlicer is an interactive viewer for contoured CCP4 map sections, which is now distributed as part of the CCP4 suite:
A set of Tcl/Tk functions that can be used to build directed graphs and render them in a Tk canvas, using the Graphviz "dot" program. It differs from tcldot (which is part of Graphviz) in that dotgraph_tcl is a pure Tcl implementation that should run on any platform that supports Tcl/Tk and "dot". However this is an early version that is still under development.
Note that the Graphviz package - which dotgraph_tcl uses to render the graphs - is not included in this download, and must be obtained and installed separately from www.graphviz.org.
You can also see the documentation for dotgraph_tcl.
hierarch_tcl is a Tcl/Tk library that is intended to form the basis for a hierarchical viewer for visualising and selecting crystals, datasets and columns in MTZ files. The project is currently under only sporadic development; the last version of the code can be picked up from:
These are small shell script utility functions that are available for download from ftp://ftp.ccp4.ac.uk/pjx/scripts
Note that after downloading a script you need to add "execute" permission to the file before it will run. Then do script -h to get usage information.
I've also written various scripts for automatically building and testing CCP4 other things, but I haven't made these publically available. If you're interested in trying them out then let me know.
There are details of some older software projects available from a separate page.
Some notes that I have written myself:
Notes on setting up automatic ssh login (23/10/07)
My experiences developing/porting applications to Windows (21/05/07)
Quick guide on using package autoloading in Tcl (Last update 01/11/02)
Notes on linking Tcl, C and Fortran (Last update 27/02/01)
A summary of the function of different Makefile targets (14/12/00)
External programming links:
A Quick and Dirty
Guide to CVS
Or look at a more comprehensive
CVS Manual
I am also developing a separate page of useful software and programming links.
Some other useful tools:
This list is a little random right now:
| PuTTY | Telnet/SSH etc client for Windows | http://www.chiark.greenend.org.uk/~sgtatham/putty/ |
| Jext | Java-based editor | http://www.jext.org/ |
| AutorunPro | Making autorun CDs under Windows | http://www.itsu.vt.edu/Workshops/CDBurning/HTML/autorun.htm |
| Graphviz | A package for visualising directed graphs | http://www.graphviz.org |
| Batik | A browser for SVG (Scalable Vector Graphics) from Apache | http://xml.apache.org/batik/ |
Go directly to my ftp area on the CCP4 server: ftp://ftp.ccp4.ac.uk/pjx
My private web area is here (username and password required)
My background is not in protein crystallography, so I have been looking for resources to supplement my meagre knowledge base. Here are a few web based resources:
For a gentle lead-in, there's a very basic set of pages on protein crystallography held here at Daresbury;
Principles of Protein Structure using the Internet: an internet-based course available from Birbeck College. The course material for the current year is password-protected, but previous years are still freely available.
Crystallography 101: an introduction to protein crystallography. This includes links to Kevin Cowtan's Book of Fourier.
Kevin Cowtan's Interactive Structure Factor Tutorial (requires Java).
An introduction to X-ray anomalous scattering by Ethan Merritt. Appears to be under construction.
Some other relevant links:
DICHROWEB: on-line Circular Dichroism analysis
EDS: the Electron Density Server at Uppsala
Bilbao Crystallographic Server: crystallographic site at the Condensed Matter Physics Department of the University of the Basque Country
Dundee PRODRG2 Server: convert descriptions of small molecules to various topology formats, including REFMAC5
There are also some links to background information about the UK's Collaborative Computation Projects (CCPs):
Here is a gallery of pictures from various conferences and meetings and whatnot:
 CCP4 at IUCr 1999, Glasgow (LtoR: Maria Turkenburg, Liz Potterton, Peter Briggs, Martyn Winn, Phil Evans, Alun Ashton (seated)) |
 CCP4 at IUCr 1999, Glasgow (LtoR: Peter Briggs, David Brown and Alun Ashton) |
 CCP4 at the ACA 2000 meeting, St Paul (LtoR: Katherine MacAuley, Alun Ashton, Peter Briggs, Harry Powell) |
 Harry and Charles at the CCP4 stand, ACA 2001 |
 CCP4 stand ACA 2001 (LtoR: Charles Ballard, Peter Briggs, Harry Powell) |
 The PDB stand ACA 2001 |
 CCP4 and the PDB get together, IUCR 2002 Geneva (LtoR: Harry Powell, Kyle Burkhardt, Christine Zardecki, Charles Ballard) |
 CCP4 people at the ACA 2003, Cincinnati (LtoR: Harry Powell, Peter Briggs, Stuart McNicholas, Roberto Steiner, Maeri Howard-Eales. Missing: Gwyndaf Evans) |
 SR User Meeting, Daresbury 2003 (LtoR: Peter Briggs, Charles Ballard, Maeri Howard-Eales, Gwyndaf Evans) |
 SR User Meeting, Daresbury 2003 Me with my poster |
 Recieving ILM Level 3 Introductory Certificate April 2004 With Ken Barr at Daresbury |
 CCP4 people at the ACA 2004, Chicago (LtoR: Gwyndaf Evans, Graeme Winter, Roberto Steiner, Peter Briggs and Stuart McNicholas. Missing: Martin Noble, Ronan Keegan, Paul Emsley) |
 Poster session at the ACA 2004, Chicago Graeme and me with our poster |
 SR User Meeting, Milton Hill House September 2004 (LtoR: Charles Ballard, Maeri Howard-Eales, Peter Briggs) |
 SR User Meeting, Milton Hill House 2004 Me with my poster |
 Structural Genomics & Proteomics EU Projects Meeting, Barcelona December 2004 (LtoR: Charles Ballard, Martyn Winn, Peter Briggs) |
 The RCSB-PDB "Art Of Science" Exhibition at Rutgers University, May 2005 |
 Visiting the RCSB-PDB at Rutgers University, May-August 2005 |
 CCP4 people at the ACA 2005, Orlando (LtoR: Graeme Winter, Stuart McNicholas, Peter Briggs and Harry Powell. Missing: Roberto Steiner, Paul Emsley) |
 Presenting a talk on CCP4 at an RUPX meeting (July 2005) |
 Speakers at the joint CCP4-RCSB PDB workshop at IUCr 2005, Florence (Back to Front, LtoR: Gwyndaf Evans, Martin Noble, Peter Briggs, Maeri Howard, Paul Emsley, Liz Potterton, Kyle Burkhardt, Martyn Winn) |
 Daresbury CCP4 group September 2005 (Back to Front, LtoR: Francois Remacle, Charles Ballard, Dan Rolfe, Maeri Howard, Peter Briggs, Martyn Winn, Norman Stein, Wanjuan Yang) |
 2nd BIOXHIT Annual Meeting, Grenoble January 2006 (LtoR: Peter Briggs and Wanjuan Yang with our poster) |
 CCP4 stand sans materials, at ACA 2006 Hawaii |
 CCP4 stand in all its glory, at ACA 2006 Hawaii |
 ACA 2006 meeting Hawaii Me with my poster |
 3rd BIOXHIT Annual Meeting, DIAMOND February 2007 (LtoR: Wanjuan Yang and Peter Briggs with our poster) |
 Daresbury CCP4 group July 2007 (Back to Front, LtoR: Francois Remacle, Norman Stein, Peter Briggs, Bill Lin, Ronan Keegan, Chris Morris, Charles Ballard, Martyn Winn, Maeri Howard, Wanjuan Yang) |
 CCP4 people at the ACA 2007, Salt Lake City |
 ACA 2007 meeting Me with my poster |
 BSR, Manchester, August 2007 (LtoR: Ronan Keegan and Peter Briggs with our poster) |
 Daresbury CCP4 group August 2008 (Back to Front, LtoR: Ronan Keegan, Graeme Winter, Chris Morris, Bill Lin, Charles Ballard, Francois Remacle, Peter Briggs, Martyn Winn, Norman Stein) More pictures |
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Other images
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[History] [Publications] [Newsletter Articles] [Conferences] [Documents]
In 1993 I gained my BSc in Theoretical Physics (First class honours) from the University of Newcastle-upon-Tyne. In September 1997 I completed a PhD in physics at the University of East Anglia (UEA), having developed computer simulations using a Monte Carlo algorithm to model the electrical transport effects within semiconductor devices. The work was performed as a CASE studentship in partnership with the DRA Great Malvern, and resulted in a number of publications.
In March 1998 I began working for CCP4 as a computational scientist, as part of the core group based at Daresbury. Initially my work focused on providing basic maintenance and development of the core suite and the provision of support for the user community. I also edited the CCP4 Newsletter on Protein Crystallography until 2001, and between October 1998 to March 1999 I was responsible for liaising with CCP4's commercial customers (prior to the appointment of the CCP4 administrative assistant).
I was responsible for managing releases of the CCP4 software suite from October 2001 to August 2004, during which time I coordinated three releases: 4.1 (January 2001), 4.2 (April 2002) and 5.0 (May 2004), plus the subsequent patch releases. I am still playing an active role as a joint coordinator of the software releases (alongside Martyn Winn and Charles Ballard), most recently with CCP4 6.0.
Over the period March 1998 to November 2005 I actively provided user support via the CCP4 helpdesk. I am currently helping to support the next generation of CCP4 staff in undertaking this activity, along with other senior group members, as well as continuing to provide user support directly.
(Details of some of these and other "defunct" activities can be found here.)
Currently I have a number of key responsibilities within the Daresbury group:
Maintaining and developing CCP4i, the CCP4 graphical user interface (since March 2001)
Coordinating the CCP4 contribution to the BioXHIT project
Joint coordination of releases of the CCP4 software suite to the user community
Maintaining and developing automated test scripts which run nightly builds of the suite on a variety of UNIX and Linux platforms
In addition to this I contribute to the group's activities in a number of other ways:
Development of the core suite through contributions to the CCP4 core libraries, the MapSlicer program, and various other utilies and libraries (see the section on software).
Active participation in CCP4's promotional and education activities, through attendence at various international conferences and meetings. This has included organising and manning exhibition stands, speaking at workshops, presenting posters at meetings, and co-organising educational workshops. I organised the CCP4 user questionnaire at the 2006 Study Weekend in Leeds.
Assist in the provision of user support and code maintenance for the suite alongside other CCP4 staff.
In October 2004 I was promoted within CCLRC, and took on management responsibilities for three CCP4 staff members at Daresbury in the period 2004 to 2008. In the summer 2005 I spent three months based at the RCSB PDB at Rutgers University, working on various improvements to the CCP4 software for deposition.
In October 2005 I transferred with the rest of CCP4 from the Biology and Medicine College of the Synchrotron Radiation Department to the Computational Science and Engineering Department at CCLRC Daresbury Laboratory. In April 2007 CCLRC merged with PPARC to become the Science & Technology Facilities Council.
List of training events attended (incomplete)
Index of Powerpoint poster files (under construction)
Guide to using PISA and notes on understanding the PISA sym ids (August 2006)
Results from a user questionnaire distributed at CCP4 Study Weekend 2006 (PDF format)
Notes on Twinning and CCP4 (7/7/2005)
Summary of a meeting about CCP4 Standard Icon Library and GUI Style Guide (9/4/2005)
Report from CCP4 workshop at ACA 2003 (Cincinnati) (MS Word format)
Please note that STFC is not responsible for the content of external sites!
Useful links:
A guide to emoticons
(STFC only) DL Taxi Bookings Page
Some places:
Other stuff: