This page links to various projects and documents which are no longer relevant but may still be useful.
[Old Projects] [Old Documents] [Old Newsletter Stats]
I was responsible for managing the releases of the CCP4 software suite from October 2001 to August 2004, during which time I coordinated three major releases: 4.1 (January 2001), 4.2 (April 2002) and 5.0 (May 2004), plus the subsequent patch releases.
For general information about the most recent releases, there is a page for software developers and contributors about the releases here:
There are some older documents that might also be relevant, although most likely are only of historical interest:
The test web forms for platform specific downloads can still be accessed from here:
however is likely that over time these pages will cease to work correctly.
As of CCP4 6.0 these prototypes were superceded by a different implementation in PHP in collaboration with Francois Remacle and other CCP4 staff:
The AREAIMOL program calculates accessible surface areas of protein structures. One of the first tasks that I worked on at CCP4 was the incorporation of the supplementary programs RESAREA, WATAREA and DIFFAREA into the original program. After that I tried sporadically to develop the program (for example adding a feature to look for "disconnected" regions of surface area). I had hoped to develop the program further to detect cavities but this work remained unfinished.
I also wrote a newsletter article comparing AREAIMOL with the SURFACE program, and in 2003 I developed a CCP4i task interface for the program which was released as part of CCP4 v5.0.
Details of planned modifications to the heavy atom phasing and refinement program MLPHARE can be found here. I looked at this project in 1998 - the modifications would have involved incorporating an algorithm due to Cullis et al that was better suited to phasing for MAD experiments than the pseudo-MIR approach which was (and continues to be) used. Unfortunately I didn't make much practical progress and the project was shelved (however at least one minor new feature was implemented as a result).
This is a C-language "parser" to replace the core Fortranic PARSER routines, and which become part of the core CCP4 libraries in CCP4 version 5.0. My original documentation is probably out of date but is vastly superior to the officially distributed version.
This was my first real Tcl/Tk program - a utility to make up DAT or Exabyte tapes of the CCP4 distribution, back in the days when we still supplied the suite to commercial customers using those media. Unfortunately I'm not sure what happened to the actual Tcl/Tk code.
Another of my early jobs was to install a selection of crystallographic software on dlpx1 at Daresbury Lab. Although I'm not responsible for this anymore some of the information is still relevant.
Access statistics for Newsletter 37: 1st October 1999 to 4th April 2000
|Article||No. of accesses|
|Circular Dichrosism and X-tallography:||239|
|Ab Initio Phasing:||358|
(There were stats for Newsletter 38 too but the counters were broken after a server upgrade...)
Access statistics for Newsletter 39: 26th March 2001 to 4th October 2002
|Article||No. of accesses|
|Lapack in CCP4 4.1:||464|
|Annotated Diffraction Data:||279|
|CCP4 molecular graphics:||730|
|Vector search methods:||353|
|PX Specialist Users Group Meeting:||292|
|ML Refinement of Atomic Models using Least squares criterion:||417|
|Efficient calculation of 2nd derivative matrix:||839|
|DL PX data collection workshop:||488|
|Improvement of noisy maps:||339|
|Multiple rotation function:||273|
|Open source programming environment for MM xtallography:||1508|
|CCP4/Max-inf refinement workshop:||369|