ccp4 study weekend 2013 “molecular replacements”
DESCRIPTION
What’s new in CCP4 "What's new in CCP4 6.3.0" "PiMS Update" Ronan Keegan, STFC Rutherford Appleton Laboratory "PiMS Update" Chris Morris, STFC Daresbury Laboratory "New features in Mosflm and iMosflm" Harry Powell, MRC Cambridge "What's new in Crank" Pavol Skubak, Leiden University "Modelling around 10Å resolution using ARP/wARP" Philipp Heuser, EMBL HamburgTRANSCRIPT
CCP4 Study Weekend 2013 Molecular Replacements Whats new in CCP4
"What's new in CCP4 6.3.0" "PiMS Update"
Ronan Keegan, STFC Rutherford Appleton Laboratory "PiMS Update"
Chris Morris, STFC Daresbury Laboratory "New features in Mosflm and
iMosflm" Harry Powell, MRC Cambridge "What's new in Crank" Pavol
Skubak, Leiden University "Modelling around 10 resolution using
ARP/wARP" Philipp Heuser, EMBL Hamburg Bytes Lunchtime Bytes Coot -
P. Emsley/B. Lohkamp
CCP4mg-S. McNicholas MrBUMP / AMPLE-R. Keegan/M. Winn
Xia2/Diamond-G. Winter/P. Hathaway Aimless / Pointless-P. Evans
Mosflm / iMosflm-H. Powell/O. Johnson Phaser-R. Oeffner Buccaneer /
Nautilus (5th of January only) -K. Cowtan Crank(4th of January
only) -P. Skubak PiMS -C. Morris Balbes-F. Long Refmac /
ProSMART-G. Murshudov/R. Nicholls Bytes Research Complex at Harwell
STFC Rutherford Appleton Laboratory
Whats new in CCP Ronan Keegan Research Complex at Harwell STFC
Rutherford Appleton Laboratory About CCP4 CCP4 stands for
Collaborative Computational Project Number 4 One of several CCPs
set up in the UK to advance and support scientific software
development CCP4 was set up in the late 1970s to bring together the
leading developers of software in the field of protein X-ray
crystallography in the UK The aim was to assemble a comprehensive
collection of software to satisfy the computational requirements of
the relevant UK groups Hosted by the Science and Technology
Facilities Council (STFC)
Part of the Research Complex at Harwell (RCaH) next door to Diamond
CCP4 funded by: Biotechnology and Biological Sciences Research
Council (BBSRC) Medical Research Council (MRC) Industrial funding
CCP4 Core Group (Oxford): CCP4 Maintain and support software
suite
Application and infrastructural software developments Collaborate
with Diamond on software deployment on the beamline Educational
outreach Maintaining CCP4 resources such as the CCP4 bulletin board
CCP4 Core Group (Oxford): Cambridge: Cambridge CCP4
Maintain and support software suite Application and infrastructural
software developments Collaborate with Diamond on software
deployment on the beamline Educational outreach Maintaining CCP4
resources such as the CCP4 bulletin board Cambridge: Laboratory of
Medical Biology Data processing software - Mosflm, Aimless
Refinement software Refmac Model building - Coot University of
Cambridge Phaser group Cambridge CCP4 Core Group (Oxford):
Cambridge: University of York: York Cambridge
Maintain and support software suite Application and infrastructural
software developments Collaborate with Diamond on software
deployment on the beamline Educational outreach Maintaining CCP4
resources such as the CCP4 bulletin board Cambridge: Laboratory of
Medical Biology Data processing software - Mosflm, Aimless
Refinement software Refmac Model building - Coot University of
Cambridge Phaser group University of York: Software development
CCP4mg, Buccaneer, Nautilus CCP4 GUI2 development York Cambridge
CCP4 Core Group (Oxford): Cambridge: University of York:
Maintain and support software suite Application and infrastructural
software developments Collaborate with Diamond on software
deployment on the beamline Educational outreach Maintaining CCP4
resources such as the CCP4 bulletin board Cambridge: Laboratory of
Medical Biology Data processing software - Mosflm, Aimless
Refinement software Refmac Model building - Coot University of
Cambridge Phaser group University of York: Software development
CCP4mg, Buccaneer, Nautilus CCP4 GUI2 development Others include
the Crank group at Leiden in the Netherlands York Cambridge CCP4
CCP4 Usage The CCP4 software suite The CCP4 suite is a
comprehensive suite of software for protein crystallography New
versions of the suite are released about every 18 months New
programs Major updates to existing programs Other new features such
as changes to CCP4i interface New - Revisions to the current
release are made available through the CCP4 updates manager CCP4
Software Crystallisation Data Collection
Data Processing and Reduction Experimental Phasing Molecular
Replacement Density Modification Model Building Refinement
Structure Analysis Deposition CCP4 Releases Current Release Version
- CCP4 6.3.0
Several new programs: Aimless, Dimple, AMPLE, Zanuda, ProSMART,
Nautilus, Ensembler, Sculptor, Jligand In collaboration with the
EMBL Hamburg, ARP/wARP is now rolled with the CCP4 suite Updates to
many of the major programs Phaser, Refmac, Mosflm/iMosflm, Crank,
MrBUMP New infrastructure Downloads manager and Updates Manager
Data Processing and Reduction
Bytes iMosflm Pointless Determine point-group (& space group)
Bytes Aimless (New) Scale-symmetry-related intensities together
Produce statistics on data quality Replacement for Scala Data
Processing and Reduction
Bytes Automated data-reduction from diffraction images to merged
reflection file Dimple (New) On-beamline rapid calculation of
difference maps to ascertain success or failure of ligand binding
Experimental Phasing Bytes Bytes Crank
Automated experimental phasing pipeline Heavy atom location through
to Model Building Bytes Phaser EP Automated experimental phasing
SAD phasing Combined MR and SAD Phasing Molecular Replacement
Bytes Phaser MR Automated Maximum Likelihood method for molecular
replacement Twining Translational NCS Molrep Molecular Replacement
Phased Rotation/Translation function Multi-copy search Molecular
Replacement - Automation
Bytes MrBUMP Automated molecular replacement From model search and
preparation through to initial refinement Uses Phaser and Molrep
Now includes Model building options Bytes BALBES Automated
molecular replacement using Molrep and Refmac Custom DB with search
models monomer, domain and multimeric form BALBES Webservice
http://www.ysbl.york.ac.uk/YSBLPrograms/index.jsp
or Google forBALBES Molecular Replacement Search model
preparation
Sculptor (New) Multi-protocol search model preparation weighted
sequence similarity accessible surface area Ensembler (New)
Ensemble search model generation tool from the developers of Phaser
Molrep & Chainsaw Search model preparation using internal
sequence alignment or provided alignment Molecular Replacement Ab
initio search models
Bytes AMPLE (beta version) Generate and prepare ab initio or de
novo models using Rosetta and other software for use as search
models in molecular replacement Works well for smaller, -helical
proteins (