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Kevin Cowtan, [email protected] CCP4 DevMeet
2008
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.
Kevin Cowtan, [email protected] CCP4 DevMeet
2008
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)
Kevin Cowtan, [email protected] CCP4 DevMeet
2008
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.
Kevin Cowtan, [email protected] CCP4 DevMeet
2008
WP5
Model Building, Refinement and Ligands
Kevin Cowtan, Garib Murshudov, Paul Emsley
Raj Pannu
Nick Furnham
Kevin Cowtan, [email protected] CCP4 DevMeet
2008
WP goals from Sep 07
4 sets of goals: Buccaneer goals Refmac goals Coot goals Collaborative goals
Kevin Cowtan, [email protected] CCP4 DevMeet
2008
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
Kevin Cowtan, [email protected] CCP4 DevMeet
2008
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.
Kevin Cowtan, [email protected] CCP4 DevMeet
2008
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)
Kevin Cowtan, [email protected] CCP4 DevMeet
2008
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)
Kevin Cowtan, [email protected] CCP4 DevMeet
2008
Buccaneer
The buccaneer software for automated model
building of protein structures across a broad
range of resolutions.
Kevin Cowtan
YSBL, University of York
Kevin Cowtan, [email protected] CCP4 DevMeet
2008
Buccaneer
Buccaneer 1.0 (for CCP4 v6.1)
A few, very major developments: Buccaneer-Refmac pipeline NCS auto-completion Improved sequencing
Kevin Cowtan, [email protected] CCP4 DevMeet
2008
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)
Kevin Cowtan, [email protected] CCP4 DevMeet
2008
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)
Kevin Cowtan, [email protected] CCP4 DevMeet
2008
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.
Kevin Cowtan, [email protected] CCP4 DevMeet
2008
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)
Kevin Cowtan, [email protected] CCP4 DevMeet
2008
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: ...
Kevin Cowtan, [email protected] CCP4 DevMeet
2008
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.
Kevin Cowtan, [email protected] CCP4 DevMeet
2008
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.
Kevin Cowtan, [email protected] CCP4 DevMeet
2008
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.
Kevin Cowtan, [email protected] CCP4 DevMeet
2008
Achnowledgements
Help: JCSG data archive: www.jcsg.org Paul Emsley, Eleanor Dodson Randy Read, Clemens Vonrhein
Funding: The Royal Society
