M.D.Winn, York, March 22nd/23rd 2005

CCP4 Library Development

M.D.Winn, York, March 22nd/23rd 2005

CCP4 5.0 released with:

CMTZ, CMAP, etc. - for i/o, fine control of data, jiffy applications

other C libraries - general CCP4 utilities

MMDB - for coordinate applications and ccp4mg

Clipper - for grown-up applications

FFTw

dna_output

CCP4 Libraries

CCP4 6.0 will have:cctbxerrrr ... that’s it

M.D.Winn, York, March 22nd/23rd 2005

•Independent library distribution•Scripting interfaces (python for automation, tcl for ccp4i)•Re-write other libraries:

fftlib --> fftw

harvlib, libhtml

•Include other libraries for general use, e.g. mmut

Libraries: future directions

No definite plans ... ... possibilities:

More important:Extend library code as required by automation projectsRe-write legacy applications in cleaner / simpler way

M.D.Winn, York, March 22nd/23rd 2005

Developer's Guide to Upgrading Programs to CCP4 5.0 Libraries

http://www.ccp4.ac.uk/dev/releases/changes_for_developers_5.0.html

•libccp4 --> libccp4f, libccp4c, libmmdb

•library.h --> ccp4_sysdep.h, ccp4_errno.h

•New crystal level in MTZ header (groups datasets) - autogenerated if not present

•Column ordering by dataset

•DCELL (present since 4.1) now used by CCP4 progs

•symop.lib --> syminfo.lib

•Library reads P2, ‘P 2’, ‘P 1 2 1’, 3 -- (CCP4 progs ) will write ‘P 2’

M.D.Winn, York, March 22nd/23rd 2005

Use of new libraries

Core library (CMTZ, CMAP, CSYM, utilities)mtz2sca, bp3/crank, mapslicer + other enquiries

MMDBccp4mg, coordinate utilities

Clipperpirate, clipper utilities

cctbxphaser, pointless

M.D.Winn, York, March 22nd/23rd 2005

Coordinate Utilities

•ncont•pdbcur

summarise PDB contentsdelete H atomskeep only most probable conformationdelete atoms with occupancy < cut-off (def. 0.0)

•coord_format•assign chain IDs when blank

•pdb_merge•merge chains or keep separate

•chainsaw•poly-Ser model based on input alignment

In response to user requests, and for automated MR:

M.D.Winn, York, March 22nd/23rd 2005

Coordinate Utilities (2)

Why old-fashioned keyworded application programs?•familiar•it works•python scripts not yet migrated from developer to user ?!

At some point, migrate to use python interfaces to mmdb and mmut

Most are simple wrappers to MMDB functionality:This is as it should be ....... but user-accessibility still important.

M.D.Winn, York, March 22nd/23rd 2005

cctbx

sourceforge.net/projects/cctbx

M.D.Winn, York, March 22nd/23rd 2005

Future Release Plans

M.D.Winn, York, March 22nd/23rd 2005

Lots in the pipeline:

ccp4mg

pirate, buccaneer

new Mosflm GUI

Coot

SSM

BP3, CRUNCH

Phaser

Phil’s OO point group scorer

+ update to usual suspects

+ stuff from automation project

The shape of things to come ...

Marc

h 200

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M.D.Winn, York, March 22nd/23rd 2005

Still in the pipeline:

ccp4mg 2.0

buccaneer

new Mosflm GUI (“late summer 05”)

Phaser 2.0

pointless (available now)

Acorn

+ stuff from automation projectMedium term:

ccp4i back-end: database handlerreplacement of legacy programs

The shape of things to come ...

M.D.Winn, York, March 22nd/23rd 2005

To re-write or junk:

act, angles, contact, distang

coordconv

mtz2various, xdldataman

mtzmnf, mtzMADmod, freerflag

restrain

surface/volume

MDW’s hitlist

Marc

h 200

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M.D.Winn, York, March 22nd/23rd 2005

Long-term issuesChange of emphasis to modern tools.E.g. function objects accessed from applications, scripts, MG.

What are boundaries to graphics, automation, traditional suite ??

Databases are great. Do we make this a dependency of CCP4?

Simplify or expand GUI?

Deal with different GUIs for automation ....

Workflows.

Flexibility vs. focus. Marc

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M.D.Winn, York, March 22nd/23rd 2005

CCP4 Licence Status

M.D.Winn, York, March 22nd/23rd 2005

Academic licence

Commercial licence

Unlicenced users ....Expires on 31st March 2005New licence available soon:

New licence available soon:

M.D.Winn, York, March 22nd/23rd 2005