ccp4 helpdesk: [email protected] what’s new in ccp4 6.0? martyn winn ccp4 cclrc daresbury laboratory...

CCP4 helpdesk: [email protected]

What’s New in CCP4 6.0?Martyn Winn

CCP4CCLRC Daresbury Laboratory

Cheshire


Background


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 2006Version 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.phpBulletin Board http://www.ccp4.ac.uk/ccp4bb.phpNewsletters: http://www.ccp4.ac.uk/newsletters.php


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 …)


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)


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

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


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


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


Kevin Cowtan, YorkClipper

• 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

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

New core programs: pirate


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

Example of 1mr6 used as a template for 1tgx (38% sequence identity)

Unmodified template Chainsaw template Polyalanine template


New core CCP4i tools and features

“Greyed out” tasks• indicate that you need to install underlying software first e.g. SHELX

Database Search/Sort Tool Quick switch between projects

Top level help• split into topics

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


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


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/


Phaser 1.3

Phaser website:http://www-structmed.cimr.cam.ac.uk/phaserhttp://www-structmed.cimr.cam.ac.uk/phaser/

• 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)

• Full CCP4i interface also provided


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 alsohttp://www.ysbl.york.ac.uk/~emsley/coot/


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)


Beyond CCP4 6.0


Ongoing developments within CCP4: programs

Available now:

• MrBUMP: automated Molecular Replacementhttp://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


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/


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)


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

TLS Refinement


Displacement of atom (position r w.r.t. origin O) in rigid body:

u t + r

Achieve parameter reduction by constraining atomic displacements to rigid-body model (other models possible):


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)


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] what’s new in ccp4 6.0? martyn winn ccp4 cclrc daresbury laboratory...

Documents

ccp4 helpdesk

nonccp4 programs

ccp4 suite

ccp4 website

ccp4 software suite

core ccp4 equivalent

conversion programs

minor programs