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Kevin Cowtan, DevMeet CCP4 Wiki ccp4wiki.org Maintainer: YOU.

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Presentation on theme: "Kevin Cowtan, DevMeet CCP4 Wiki ccp4wiki.org Maintainer: YOU."— Presentation transcript:

1 Kevin Cowtan, cowtan@ysbl.york.ac.ukCCP4 DevMeet 2008cowtan@ysbl.york.ac.uk CCP4 Wiki ccp4wiki.org Maintainer: YOU

2 Kevin Cowtan, cowtan@ysbl.york.ac.ukCCP4 DevMeet 2008cowtan@ysbl.york.ac.uk CCP4 wiki Original aims (as I understand them): Provide a framework for updating the documentation. Provide a forum for useful BB discussions to be collected.

3 Kevin Cowtan, cowtan@ysbl.york.ac.ukCCP4 DevMeet 2008cowtan@ysbl.york.ac.uk CCP4 wiki Provide a forum for useful BB discussions to be collected. Addressed by Kay Diedrichs with the CCP4 community wiki! Less work for us! Publicly editable. (vs our more restricted aims) Independent. (No legal ramifications for us)

4 Kevin Cowtan, cowtan@ysbl.york.ac.ukCCP4 DevMeet 2008cowtan@ysbl.york.ac.uk CCP4 wiki Provide a framework for updating the documentation. A wiki has been setup and configured using an external web hosting service. Took 2 attempts, but the new host seems good. Don't know about support, I haven't needed it! Populated with a few demonstration pages to provide ideas and inspiration.

5 Kevin Cowtan, cowtan@ysbl.york.ac.ukCCP4 DevMeet 2008cowtan@ysbl.york.ac.uk

6 Kevin Cowtan, cowtan@ysbl.york.ac.ukCCP4 DevMeet 2008cowtan@ysbl.york.ac.uk

7 Kevin Cowtan, cowtan@ysbl.york.ac.ukCCP4 DevMeet 2008cowtan@ysbl.york.ac.uk

8 Kevin Cowtan, cowtan@ysbl.york.ac.ukCCP4 DevMeet 2008cowtan@ysbl.york.ac.uk

9 Kevin Cowtan, cowtan@ysbl.york.ac.ukCCP4 DevMeet 2008cowtan@ysbl.york.ac.uk

10 Kevin Cowtan, cowtan@ysbl.york.ac.ukCCP4 DevMeet 2008cowtan@ysbl.york.ac.uk

11 Kevin Cowtan, cowtan@ysbl.york.ac.ukCCP4 DevMeet 2008cowtan@ysbl.york.ac.uk

12 Kevin Cowtan, cowtan@ysbl.york.ac.ukCCP4 DevMeet 2008cowtan@ysbl.york.ac.uk

13 Kevin Cowtan, cowtan@ysbl.york.ac.ukCCP4 DevMeet 2008cowtan@ysbl.york.ac.uk

14 Kevin Cowtan, cowtan@ysbl.york.ac.ukCCP4 DevMeet 2008cowtan@ysbl.york.ac.uk CCP4 Wiki And Kevin said... 'Go forth and edit'

15 Kevin Cowtan, cowtan@ysbl.york.ac.ukCCP4 DevMeet 2008cowtan@ysbl.york.ac.uk WP5 Model Building, Refinement and Ligands Kevin Cowtan, Garib Murshudov, Paul Emsley Raj Pannu Nick Furnham

16 Kevin Cowtan, cowtan@ysbl.york.ac.ukCCP4 DevMeet 2008cowtan@ysbl.york.ac.uk WP goals from Sep 07 4 sets of goals: Buccaneer goals Refmac goals Coot goals Collaborative goals

17 Kevin Cowtan, cowtan@ysbl.york.ac.ukCCP4 DevMeet 2008cowtan@ysbl.york.ac.uk WP goals from Sep 07 Buccaneer goals: Improve chain numbering (done, 6.1) Improve sidechain building (done, 6.1) Fix model position (done, 6.1) Implement sequence verification

18 Kevin Cowtan, cowtan@ysbl.york.ac.ukCCP4 DevMeet 2008cowtan@ysbl.york.ac.uk WP goals from Sep 07 Refmac goals: Better communication with Coot. (done) Release refinement against SAD target. (6.1- uns) First release of JLigand. (6.1?, to be released) Twin refinement. (to be released) Flexible NCS, occupancy, B restraints. GUI pipeline options for waters, blast, etc. Sensible GUI defaults for TLS.

19 Kevin Cowtan, cowtan@ysbl.york.ac.ukCCP4 DevMeet 2008cowtan@ysbl.york.ac.uk WP goals from Sep 07 Coot goals: Integrate wincoot. (done) Test new Ramachandran restraint idea. (nearly) Use MMDB link-reading code. (license) Rapper wrapper. (nearly)

20 Kevin Cowtan, cowtan@ysbl.york.ac.ukCCP4 DevMeet 2008cowtan@ysbl.york.ac.uk WP goals from Sep 07 Collaborative goals: Decide what to do about ligand developments.  PE/GM. Buccaneer/refmac recycling to make better use of refmac.  KC/GM teaching, other work. Make contact with new Rapper developer.  (visa issues)

21 Kevin Cowtan, cowtan@ysbl.york.ac.ukCCP4 DevMeet 2008cowtan@ysbl.york.ac.uk Buccaneer The buccaneer software for automated model building of protein structures across a broad range of resolutions. Kevin Cowtan YSBL, University of York cowtan@ysbl.york.ac.uk

22 Kevin Cowtan, cowtan@ysbl.york.ac.ukCCP4 DevMeet 2008cowtan@ysbl.york.ac.uk Buccaneer Buccaneer 1.0 (for CCP4 v6.1) A few, very major developments: Buccaneer-Refmac pipeline NCS auto-completion Improved sequencing

23 Kevin Cowtan, cowtan@ysbl.york.ac.ukCCP4 DevMeet 2008cowtan@ysbl.york.ac.uk Buccaneer: Future Buccaneer 1.1 (ready for release after 6.1) Improved linking of nearby chains Improved numbering of output chains Improved sidechain fitting:  Use Richardson rotamer library  Favour more probable sidechain rotamers  Rudimentary chi1 refinement  Prune clashing side chains Optionally fix the model in the ASU General performance improvements (33%) Multi-threading (for dual/quad core machines)

24 Kevin Cowtan, cowtan@ysbl.york.ac.ukCCP4 DevMeet 2008cowtan@ysbl.york.ac.uk Buccaneer: Future Buccaneer 1.2+ Rebuilding cis-peptides, pep-flips, pep-rots. Sequence verification. Use of Se atoms, MR model in sequencing. Loop building. B-factor refinement. (Also for coot)

25 Kevin Cowtan, cowtan@ysbl.york.ac.ukCCP4 DevMeet 2008cowtan@ysbl.york.ac.uk Buccaneer: Comparisons With ARP/wARP: From my tests and user reports buccaneer will build most structures which ARP/wARP will build.  But ARP/wARP gets a lower R-factor.  The benefit of using individual atoms. Buccaneer will also build structures where ARP/wARP fails.  Particularly with good data but poor resolution.  The benefit of using larger rigid groups.

26 Kevin Cowtan, cowtan@ysbl.york.ac.ukCCP4 DevMeet 2008cowtan@ysbl.york.ac.uk Buccaneer: Comparisons Citations: Still only 4. (structures published without citation - grrr...) User reports: 2 novel structures built at 3.6A 1 commercial MR structure rebuilt at York at 3.1A (Buccaneer/Coot/Quanta)

27 Kevin Cowtan, cowtan@ysbl.york.ac.ukCCP4 DevMeet 2008cowtan@ysbl.york.ac.uk Buccaneer: Comparisons User reports: Pietro Roversi:  Used for 2vix.  Recommends it for the range 2.6-3.2A. Tassos Perrakis:  Currently using it for tricky MR rebuild at 2.7A Qui Ping Xu (JCSG):  Builds 2.8A structures where RESOLVE fails.  Incorporate in JCSG pipeline. Clemens Vonrhein:...

28 Kevin Cowtan, cowtan@ysbl.york.ac.ukCCP4 DevMeet 2008cowtan@ysbl.york.ac.uk Buccaneer and density modification Clemens: Iteration of buccaneer and solomon shows promise. Traditional density modification still has much to offer. By contrast with Pirate: Other developers have not on the whole had much success with Pirate. The statistical dm calculation is far harder to analyse. A development black hole.

29 Kevin Cowtan, cowtan@ysbl.york.ac.ukCCP4 DevMeet 2008cowtan@ysbl.york.ac.uk Buccaneer and density modification Parrot: Traditional density modification (c.f. Solomon), with some new elements:  MLHL target (under development for use in coot).  Refine alpha, beta, and the parameters of the solvent mask against the free LLK. Later, more advanced elements can be introduced. Prior density information from:  Atomic model from MR/Buccaneer  NCS (automated), from either HA or partial model.

30 Kevin Cowtan, cowtan@ysbl.york.ac.ukCCP4 DevMeet 2008cowtan@ysbl.york.ac.uk Buccaneer and density modification Parrot: A stand-alone density modification program:  Like 'dm', but more automated.  Fast. A step within buccaneer:  No prior density modification step required.  Recycling allows model to be used as prior density and to identify NCS.

31 Kevin Cowtan, cowtan@ysbl.york.ac.ukCCP4 DevMeet 2008cowtan@ysbl.york.ac.uk Achnowledgements Help: JCSG data archive: www.jcsg.org Paul Emsley, Eleanor Dodson Randy Read, Clemens Vonrhein Funding: The Royal Society

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