What’s New in CCP4 6.0?
Martyn Winn
CCLRC Daresbury Laboratory
CCP4 helpdesk: ccp4@dl.ac.uk
CCP4 helpdesk: ccp4@dl.ac.uk
Collaborative Computational Project Number 4
CCP4 software suite:
• Scope: covers data processing through to refinement and validation
• Modular: lots of individual programs sharing data via common file formats
• Keywords control program function and provide additional data
• Redundancy in choice of programs
• Also has a graphical interface CCP4i
Version 6.0 was released in February 2006
Version 6.0.1 was released in June 2006
CCP4 website:
Old workshops and course: http://www.ccp4.ac.uk/ccp4course.php
Bulletin Board
CCP4 helpdesk: ccp4@dl.ac.uk
Scope of the CCP4 Suite
• ~200 (?) programs covering all aspects of PX structure determination
• Relatively small subset are significant for most users, e.g.:
• Data processing and reduction (mosflm, scala, truncate ...)
• Experimental phasing (mlphare, acorn, rantan, oasis, bp3 ...)
• Molecular replacement (amore, molrep, phaser)
• Density modification (dm, solomon, pirate)
• Refinement (refmac5, sketcher)
• Graphics and building (ccp4mg, coot)
• Validation and analysis (sfcheck, procheck …)
• Utility and conversion programs (e.g. fft, cad, revise …)
CCP4 helpdesk: ccp4@dl.ac.uk
Graphical User Interface CCP4i
• Sits on top of programs
• Hides details of individual programs
• User not locked in
• Allows mix-and-match approach
• Philosophy:
• “Task-driven” rather than “program-driven”
• Interfaces to tasks use “natural language” approach
• e.g.
• Key features:
• Easy-to-use interfaces to major programs and utilities
• Integrated tools for file viewing and basic project management
• Customisable
• Integrated help system
• Some non-CCP4 programs also interfaced (e.g. ARP/wARP, SHELX)
CCP4 helpdesk: ccp4@dl.ac.uk
Navigating the suite
Key questions:
• Which program(s) do I need?
• How do I run it/them?
Documentation (http://www.ccp4.ac.uk/docs.html):
• Roadmaps
• Tutorials (html)
• Individual program documentation (html)
• Function index
• General background on twinning, reindexing, …
• Postscript manual
• Slightly dated but still useful
• Content distinct from program documentation
Runnable example scripts
CCP4 helpdesk: ccp4@dl.ac.uk
Automated download and install for 6.0
Downloads divided into a number of packages:
• Core CCP4 (equivalent to v5.0)
• Phaser and CCTBX
• CCP4mg
• Coot
• plus dependencies (“tools”): Tcl/Tk/BLT, Python
• For Macintosh and Windows: use the self-extracting packages
• On Windows:
• remove any previous installation first
• admin privileges are required to install
• For Linux, Unix variants
• use install.sh script in download archive to install automatically
CCP4 6.0
CCP4 helpdesk: ccp4@dl.ac.uk
Updated programs in core CCP4 6.0
New versions of major programs:
• REFMAC 5.2.0019
• MOLREP 9.0.09
• SFCHECK 7.0.18
• MOSFLM 6.2.5
Updates to minor programs:
• PDBCUR (PDB editing tool):
Summarise model content, choose most likely conformation,
delete hydrogens/atoms based on occupancy threshold …
Outputs Kantardjieff & Rupp resolution-based probabilities for
number of molecules in ASU
CCP4 helpdesk: ccp4@dl.ac.uk
New programs in core CCP4
Superpose (Eugene Krissinel, EBI)
• secondary-structure based alignment program
• aligns first on secondary structure then on Cα atom positions
• outputs the transformation matrix plus per-residue listing of the quality
of the match & identification of the secondary structure
BP3 (Raj Pannu, Leiden)
• heavy-atom refinement and phasing program
• uses multivariate likelihood functions to refine and phase heavy and/or
anomalously scattering substructure (i.e. S/MIR(AS) and S/MAD)
• “Jiffy” program to combine the content from two PDB files
CCP4 helpdesk: ccp4@dl.ac.uk
New core programs: pirate
Kevin Cowtan, York
• a set of crystallographic software libraries developed by Kevin Cowtan
• see http://www.ysbl.york.ac.uk/~cowtan
• statistical phase improvement (replacement for dm)
•Nb: executables are actually called cpirate and cmakereference
Other Clipper utilities in 6.0
• see e.g. the Clipper Utilities module of CCP4i
CCP4 helpdesk: ccp4@dl.ac.uk
New core programs: pirate
• General categorisation of protein/solvent (order/disorder vs
• Uses phases from known reference structure with features similar to
unknown structure (use makereference program for this)
• Doesn’t require knowledge of solvent content
• Pirate NCS. Novel feature: each molecule gets its own mask based on
agreement with NCS.
• Pirate in 6.0. Slower than DM. Dependent on quality of HL coeffs,
because they describe noise used to generate noisy reference structure.
• For large reference structures, not so sensitive to choice. Might want
something else for protein-DNA. Otherwise 1ajr.
• New version of pirate in August
CCP4 helpdesk: ccp4@dl.ac.uk
MR model preparation: chainsaw
Molecular replacement model preparation utility that mutates a
template PDB file according to a sequence alignment.
– Prunes non-conserved residues back to the gamma atom
– Removes “unlikely” parts of model
– Preserves more atoms than in polyalanine model
Unmodified template
Chainsaw template
Polyalanine template
Example of 1mr6 used as a template for 1tgx (38% sequence identity)
CCP4 helpdesk: ccp4@dl.ac.uk
New core CCP4i tools and features
“Greyed out” tasks
Database Search/Sort Tool
• indicate that you need
to install underlying
software first e.g.
Top level help
• split into topics
Quick switch
between projects
CCP4 helpdesk: ccp4@dl.ac.uk
Custom job view colours
New interfaces in CCP4i
• Suite of programs for automated structure solution
based on the CCP4i infrastructure
• Current version supports SAD, SIR and SIRAS
• Covers steps from scaled/merged data to density
• “Translucent box” – also intended as teaching aid
• Interface to the Sheldrick SHELX C/D/E programs for heavy atom location,
phasing and refinement
• Allows programs to be run as a pipeline or individually
• Performs file format conversions and extracts useful graphs from output
• Not all options currently interfaced
• NB#1 scala interface (Scale and merge intensities task) can now outputs data
in a form suitable for SHELX and SOLVE
• NB#2 still need to fetch and install SHELX programs yourself
CCP4 helpdesk: ccp4@dl.ac.uk
New/updated interfaces in CCP4i
Interfaces for new programs:
• Pirate and Clipper utilities
• BP3 (in the Experimental Phasing module)
• Superpose
• Chainsaw (“Create Search Model” in Molecular Replacement module)
• Also a launcher task for CCP4mg launcher (see later)
Plus updates to existing tasks, for example:
• areaimol (accessible surface area calculation):
generate pairwise area differences for arbitrary groups of chains
• matthews_coef and pdbset/pdbcur:
accommodate new/extended functionality
CCP4 helpdesk: ccp4@dl.ac.uk
CCP4mg: presentation graphics & analysis
CCP4 molecular graphics package compatible with
CCP4 environment
• focused on structure analysis and presentation
• view coordinates (ball & stick, ribbons, spheres…)
• show surfaces (electrostatic, solvent accessible …)
• display maps (electron density…)
• examine local environment, contacts, packing
• structure superposition
• CCP4 6.0 includes version 0.12
• See http://www.ysbl.york.ac.uk/~ccp4mg/
CCP4 helpdesk: ccp4@dl.ac.uk
Phaser 1.3
• Maximum likelihood based phasing
• Current version has methods for
molecular replacement (experimental
phasing functions under
• uses ensembles of many models
weighted by estimates of similarity
• Allows searching for multiple
molecules in multiple spacegroups
• Requires CCTBX libraries (included)
Phaser website:
• Full CCP4i interface also provided
CCP4 helpdesk: ccp4@dl.ac.uk
Model building & validation: Coot 0.0.33
Platform for semi-automated model building and validation tools, including:
• idealisation
• real-space refinement
• manual rotation/translation
• rigid body fitting
• ligand and solvation search
• mutations
• rotamer analysis & fitting
• Ramachandran plots and
other validation tools e.g.
geometry analysis
• interface to REFMAC
See also
CCP4 helpdesk: ccp4@dl.ac.uk
Calculate f’/f’’: Chooch
• Determine values of anomalous
scattering factors from raw
fluorescence spectra
• Pinpoint positions of f’ minimum
and f’’ maximum
• Chooch version 5.02 in CCP4 6.0
• Not currently interfaced in CCP4i
CCP4 helpdesk: ccp4@dl.ac.uk
Beyond CCP4 6.0
CCP4 helpdesk: ccp4@dl.ac.uk
Ongoing developments within CCP4: programs
Available now:
• MrBUMP: automated Molecular Replacement
• iMOSFLM: new interface to MOSFLM
Other on-going developments within core group:
• HAPPy (Heavy Atom Phasing in Python):
• an automated Experimental Phasing pipeline
• CCP4i/BIOXHIT project database:
• expanding the data stored by CCP4i and making it available to
other programs
• an automated data processing system
CCP4 helpdesk: ccp4@dl.ac.uk
iMOSFLM: new MOSFLM user interface
MOSFLM is the CCP4 diffraction
image integration program
• Suffered from a clunky X11
interface – difficult to use (and
• Meant that MOSFLM won’t work
on MS Windows
• completely redesigned user
• Modern, better controls, easier
to learn and use
Beta version available at:
CCP4 helpdesk: ccp4@dl.ac.uk
Some future programs
More Clipper-based programs (Kevin Cowtan):
• Buccaneer: statistical chain-tracing with ML target
• Privateer: refine crude low-resolution structures
• See http://www.ysbl.york.ac.uk/~cowtan/
• Spacegroup determination/(re)indexing for unmerged reflection
data (Phil Evans)
• For given cell and lattice type, list alternative indexing and/or cell
parameters (Phil Evans)
• Automated MR using REFMAC, MOLREP and SFCHECK (Garib
Murshudov, Alexei Vagin and Fei Long)
CCP4 helpdesk: ccp4@dl.ac.uk
TLS Refinement
CCP4 helpdesk: ccp4@dl.ac.uk
TLS Refinement
TLS parameterization allows to partly take into account
anisotropic motions at medium/low resolution (> 3.5 Å)
TLS refinement might improve refinement statistics of
several percent
TLS refinement in REFMAC5 is fast and therefore can be
used routinely
TLS parameters can be analyzed to extract physical
CCP4 helpdesk: ccp4@dl.ac.uk
Achieve parameter reduction by constraining atomic displacements
to rigid-body model (other models possible):
Displacement of
atom (position r
w.r.t. origin O) in
rigid body:
CCP4 helpdesk: ccp4@dl.ac.uk
TLS parameters
Experiment yields mean square displacements:
UTLS  <uu> = T + ST  r - r  S - r  L
T = <tt>, L = <> and S = <t> describe mean
square Translation and Libration of rigid body and
their correlation (Screw-motion).
T  6 parameters, L  6 parameters, S  8
(trace of S is undetermined)
CCP4 helpdesk: ccp4@dl.ac.uk
Atomic parameters from TLSANL
• TLS tensors  UTLS for atoms in group (ANISOU
records in XYZOUT)
• UTLS  BTLS and anisotropy A
• Also have individually refined Bres from Refmac
• BTOT = BTLS + Bres (ATOM records in
• keyword ISOOUT determines which contribution
recorded in ATOM/ANISOU
CCP4 helpdesk: ccp4@dl.ac.uk