CCP4 Version 4.0 ...
The most recent version of the CCP4 suite is 4.0, which was released in January 2000, with a minor patch
release shortly after. Below are some of the highlights in this latest version of the Suite.
Alexei Vagin’s automated program
Data harvesting means that the software used in structure solution outputs for molecular replacement.
details of the method used and the results obtained (for example, the heavy
The program utilises new approaches in data
atom sites used in phasing). processing and rotational and translation searching
to give improved molecular replacement solutions.
The information is stored in deposition files (also called harvest files) - by
the time the user is ready to deposit the model coordinates there should be Left: The enzyme D-alanine-D-lactate ligase (VanA)
a collection of such files holding details of how the model was obtained. from Enterococcus faecium BM4147 is directly
These can be sent directly to the deposition centre - thereby by-passing responsible for the biosynthesis of alternate cell wall
precursors in clinically prevalent Enterococcal
much of the manual processing required by AutoDep.
species which are resistant to the glycopeptide
Within CCP4 4.0 the programs SCALA, TRUNCATE, MLPHARE, REFMAC and The structure of VanA was determined from data extending to 2.5Å with the aid of MOLREP. The
RESTRAIN have been upgraded to produce harvest files. structure of the active site was found to differ significantly from the model previously assumed (from
the functionally related D-Alanyl-D-Alanine ligase from E. coli), leading to a revised understanding of
For more information on Data Harvesting see CCP4 Newsletters 37 the mechanism for Vancomycin resistance.
(October 1999) and 35 (July 1998).
Reference: Roper, D.I., Huyton T., Veguine A., & Dodson G. (2000) “The Molecular Basis of
Vancomycin Resistance in Clinically Relevant Enterococci. Crystal Structure of D-alanyl-D-lactate
ligase (VanA)” PNAS (in press)
Right: Surface complementarity between influzena virus tern
N9 neuraminidase (right) and the NC10 single-chain antibody
variable domain (left), based on the coordinates of the PDB
entry 1A14. The interface is shown opened out in book-like Mike Lawrence’s program for determining
fashion, with Sc values coloured from white (Sc = 0.0) to blue
(Sc=1.0). Regions shown in red have Sc<0.0, or lie outside of
the shape complementarity statistic Sc of
the buried area considered for the calculation of Sc. two interacting molecular surfaces.
The picture was generated using the program SC , and Reference: Lawrence, M.C. & Coleman, P.M. (1993)
displayed using GRASP (Nichols, A.J., (1993) Biophys. J. 64, “Shape complementarity at protein/protein interfaces”
A116.) J. Mol. Biol. 234, 946-950.
ccp4i: CCP4 graphical interface
Program using direct methods to break the intrinsic phase
CCP4i provides a simple graphical user ambiguity in OAS and SIR problems (Q. Hao, Y.X. Gu, C.D.
interface for running the CCP4 Zheng & H.F. Fan).
Direct Methods on their own require high
programs, plus a set of utilities for easy resolution - OASIS however has been
viewing of standard CCP4-format files, successful at moderate resolution (1.4 -
a database facility to assist with project 2.5Å).
management, and an integrated help Left: Rusticyanin is a type-1 blue copper
system. protein (17kDa) and is thought to be a
principal component in the iron respiratory
CCP4i version 1.1.1 is now officially electron transport chain of Thiobacillus
part of the main suite and is no longer ferrooxidans.
distributed separately. The structure of rusticyanin was solved with
the aid of the OASIS program using one
wavelength anomalous scattering data at 2.1Å resolution collected near the copper
Reference: Harvey, I., Hao, Q., Duke, E.M.H., Ingledew, W.J. & Hasnain, S.S.
Updated programs (1998) Acta. Cryst. D54 629-635 “Structure Determination of a 16.8 kDa Copper
Protein at 2.1Å Resolution Using Anomalous Scattering Data with Direct Methods.”
•DM 2.0.5 - density modification package.
•SCALA 2.7.2 - scale together multiple observations of reflections.
•TOPP 6.5 - automatic topological and atomic comparison program.
•AMORE - a major new version of Jorge Navaza’s molecular CCP4NT : a preliminary version is now available which allows
replacement package. the CCP4 suite to run under Microsoft NT
•RASMOL 2.7.1 - updated version of the molecular visualisation REFMAC : the current β-release of Refmac includes: refinement of
program. TLS parameters; bulk solvent correction; new dictionary. It also
•SFCHECK 5.3.4 - program for assessing agreement between atomic dispences with the need to run PROTIN.
model and X-ray data. MAPSLICE : viewing contoured sections through maps
•ARP_WARP 5.0 - popular automated refinement program. (replacement for NPO)
CCP4 4.1 : the next release will include D*TREK2MTZ, CAVENV,
Plus: updated versions of AREAIMOL, DETWIN, SCALEIT, ROTGEN, FFFEAR, MOSFLM and others
TRUNCATE and others