CCP4 Version 4'0 '''

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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.
molrep
Data harvesting
Alexei Vagins automated program for molecular
replacement.
Data harvesting means that the software used in
structure solution outputs details of the method
used and the results obtained (for example, the
heavy atom sites used in phasing). 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 a collection of such files holding
details of how the model was obtained. These can
be sent directly to the deposition centre -
thereby by-passing much of the manual processing
required by AutoDep. Within CCP4 4.0 the
programs SCALA, TRUNCATE, MLPHARE, REFMAC and
RESTRAIN have been upgraded to produce harvest
files. For more information on Data Harvesting
see CCP4 Newsletters 37 (October 1999) and 35
(July 1998).
The program utilises new approaches in data
processing and rotational and translation
searching to give improved molecular replacement
solutions. Left The enzyme D-alanine-D-lactate
ligase (VanA) from Enterococcus faecium BM4147 is
directly responsible for the biosynthesis of
alternate cell wall precursors in clinically
prevalent Enterococcal species which are
resistant to the glycopeptide antiobiotic
Vancomycin.
The structure of VanA was determined from data
extending to 2.5Å with the aid of MOLREP. The
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 the mechanism for Vancomycin
resistance. 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)
sc
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
fashion, with Sc values coloured from white (Sc
0.0) to blue (Sc1.0). Regions shown in red have
Sclt0.0, or lie outside of the buried area
considered for the calculation of Sc. The
picture was generated using the program SC , and
displayed using GRASP (Nichols, A.J., (1993)
Biophys. J. 64, A116.)
Mike Lawrences program for determining the shape
complementarity statistic Sc of two interacting
molecular surfaces.
Reference Lawrence, M.C. Coleman, P.M. (1993)
Shape complementarity at protein/protein
interfaces J. Mol. Biol. 234, 946-950.
oasis
ccp4i CCP4 graphical interface
Program using direct methods to break the
intrinsic phase ambiguity in OAS and SIR problems
(Q. Hao, Y.X. Gu, C.D. Zheng H.F. Fan).
CCP4i provides a simple graphical user interface
for running the CCP4 programs, plus a set of
utilities for easy viewing of standard
CCP4-format files, a database facility to assist
with project management, and an integrated help
system. CCP4i version 1.1.1 is now officially
part of the main suite and is no longer
distributed separately.
Direct Methods on their own require high
resolution - OASIS however has been successful at
moderate resolution (1.4 - 2.5Å). Left
Rusticyanin is a type-1 blue copper protein
(17kDa) and is thought to be a principal
component in the iron respiratory electron
transport chain of Thiobacillus
ferrooxidans. 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 absorption
edge. Reference Harvey, I., Hao, Q., Duke,
E.M.H., Ingledew, W.J. Hasnain, S.S. (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.
Updated programs

• 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 Navazas
  molecular replacement package.
• RASMOL 2.7.1 - updated version of the molecular
  visualisation program.
• SFCHECK 5.3.4 - program for assessing agreement
  between atomic model and X-ray data.
• ARP_WARP 5.0 - popular automated refinement
  program.

Future developments
CCP4NT a preliminary version is now available
which allows the CCP4 suite to run under
Microsoft NT
REFMAC the current ß-release of Refmac
includes refinement of TLS parameters bulk
solvent correction new dictionary. It also
dispences with the need to run PROTIN.
MAPSLICE viewing contoured sections through
maps (replacement for NPO)
CCP4 4.1 the next release will include
DTREK2MTZ, CAVENV, ROTGEN, FFFEAR, MOSFLM and
others
Plus updated versions of AREAIMOL, DETWIN,
SCALEIT, TRUNCATE and others