What’s New in CCP4 6.0?
Martyn Winn
CCP4
CCLRC Daresbury Laboratory
Cheshire
CCP4 helpdesk: [email protected]
Background
CCP4 helpdesk: [email protected]
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:
http://www.ccp4.ac.uk/
Old workshops and course: http://www.ccp4.ac.uk/ccp4course.php
Bulletin Board
http://www.ccp4.ac.uk/ccp4bb.php
Newsletters:
http://www.ccp4.ac.uk/newsletters.php
CCP4 helpdesk: [email protected]
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: [email protected]
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: [email protected]
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/examples/unix/runnable
CCP4 helpdesk: [email protected]
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
• CHOOCH
• plus dependencies (“tools”): Tcl/Tk/BLT, Python
Installation:
• 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: [email protected]
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 …
• MATTHEWS_COEFF:
Outputs Kantardjieff & Rupp resolution-based probabilities for
number of molecules in ASU
CCP4 helpdesk: [email protected]
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)
Pdb_merge
• “Jiffy” program to combine the content from two PDB files
CCP4 helpdesk: [email protected]
New core programs: pirate
Kevin Cowtan, York
Clipper
• a set of crystallographic software libraries developed by Kevin Cowtan
• see http://www.ysbl.york.ac.uk/~cowtan
Pirate
• 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: [email protected]
New core programs: pirate
• General categorisation of protein/solvent (order/disorder vs
dense/sparse)
• 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: [email protected]
MR model preparation: chainsaw
•
Molecular replacement model preparation utility that mutates a
template PDB file according to a sequence alignment.
•
Features:
– 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: [email protected]
New core CCP4i tools and features
“Greyed out” tasks
Database Search/Sort Tool
• indicate that you need
to install underlying
software first e.g.
SHELX
Top level help
• split into topics
Quick switch
between projects
CCP4 helpdesk: [email protected]
Custom job view colours
New interfaces in CCP4i
Crank:
• 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
modification
• “Translucent box” – also intended as teaching aid
Shelx_cde:
• 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: [email protected]
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: [email protected]
CCP4mg: presentation graphics & analysis
CCP4 molecular graphics package compatible with
CCP4 environment
• focused on structure analysis and presentation
graphics/movies
• view coordinates (ball & stick, ribbons, spheres…)
• show surfaces (electrostatic, solvent accessible …)
• display maps (electron density…)
• examine local environment, contacts, packing
diagrams
• structure superposition
• CCP4 6.0 includes version 0.12
• See http://www.ysbl.york.ac.uk/~ccp4mg/
CCP4 helpdesk: [email protected]
Phaser 1.3
• Maximum likelihood based phasing
• Current version has methods for
molecular replacement (experimental
phasing functions under
development)
• uses ensembles of many models
weighted by estimates of similarity
• Allows searching for multiple
molecules in multiple spacegroups
• Requires CCTBX libraries (included)
Phaser website:
http://www-structmed.cimr.cam.ac.uk/phaser/
• Full CCP4i interface also provided
CCP4 helpdesk: [email protected]
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
http://www.ysbl.york.ac.uk/~emsley/coot/
CCP4 helpdesk: [email protected]
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
(coming)
CCP4 helpdesk: [email protected]
Beyond CCP4 6.0
CCP4 helpdesk: [email protected]
Ongoing developments within CCP4: programs
Available now:
• MrBUMP: automated Molecular Replacement
http://www.ccp4.ac.uk/MrBUMP
• 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
• XIA-DP:
• an automated data processing system
CCP4 helpdesk: [email protected]
iMOSFLM: new MOSFLM user interface
MOSFLM is the CCP4 diffraction
image integration program
• Suffered from a clunky X11
interface – difficult to use (and
ugly)
• Meant that MOSFLM won’t work
on MS Windows
iMOSFLM:
• completely redesigned user
interface
• Modern, better controls, easier
to learn and use
Beta version available at:
http://alf1.mrc-lmb.cam.ac.uk/~geoff/mosflm/
CCP4 helpdesk: [email protected]
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/
Pointless:
• Spacegroup determination/(re)indexing for unmerged reflection
data (Phil Evans)
Othercell:
• For given cell and lattice type, list alternative indexing and/or cell
parameters (Phil Evans)
BALBES:
• Automated MR using REFMAC, MOLREP and SFCHECK (Garib
Murshudov, Alexei Vagin and Fei Long)
CCP4 helpdesk: [email protected]
TLS Refinement
CCP4 helpdesk: [email protected]
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
significance
●
CCP4 helpdesk: [email protected]
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:
ut+r
CCP4 helpdesk: [email protected]
TLS parameters
Experiment yields mean square displacements:
UTLS  <uu> = T + ST  r - r  S - r  L
r
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
parameters
(trace of S is undetermined)
CCP4 helpdesk: [email protected]
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
XYZOUT)
• keyword ISOOUT determines which contribution
recorded in ATOM/ANISOU
lines
CCP4 helpdesk: [email protected]
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