23 rd August 2005CCP4-RCSB Workshop IUCr 2005 Florence Italy 1 N6: A Protein Crystallographic Toolbox: The CCP4 Software Suite and RCSB PDB Deposition.

Slides:

Advertisements

Similar presentations

EBank UK CCLRC Workshop February eBank and CCLRC Workshop February 2005 University of Bath.

Advertisements

CCP4 Molecular Graphics (CCP4MG)

M.D.Winn, DL, March 28th 2007 Session 4 Core activities Intro Overview: Martyn CCP4 Releases: Charles Installation issues: Francois Meetings: Maeri Python.

Management and Distribution of Chemical Data in the Protein Data Bank John Westbrook, Dimitris Dimitropoulos, Jasmine Young, Peter Rose, Philip E. Bourne.

KE’s EMu Documentation

Thematic Introduction, Aims of the Conference & Conference Run Jürgen Horschinegg Federal Ministry for Education, Science and Culture.

Planetary Science Archive PSA User Group Meeting #1 PSA UG #1  July 2 - 3, 2013  ESAC Welcome and Logistics.

26-28 th April 2004BioXHIT Kick-off Meeting: WP 5.2Slide 1 WorkPackage 5.2: Implementation of Data management and Project Tracking in Structure Solution.

1. 2 ISMB/ECCB 2004  31 July – 5 August 2004  SIGs 29 & 30 July 2004  Glasgow, Scotland,UK  Scottish Exhibition and Conference Centre.

Erice 2008 Introduction to PDB Workshop From Molecules to Medicine: Integrating Crystallography in Drug Discovery Erice, 29 May - 8 June Peter Rose

23 rd August 2005CCP4 Workshop IUCr 2005 Florence Italy 1 N6: A Protein Crystallographic Toolbox: The CCP4 Software Suite and PDB Deposition Tools IUCr.

Copyright © President & Fellows of Harvard College Ann Cullen, October 3rd, 2009 Baker Library Services Alumni Overview.

Evaluation of Structure Quality Using RCSB PDB Tools Kyle Burkhardt, Lead Data Annotator The RCSB PDB at Rutgers University.

European Network of Excellence in AI Planning Knowledge Engineering TCU in PLANET part 2 September, 2001 Lee McCluskey, University.

CCP4mg Liz Potterton, Stuart McNicholas, Martin Noble, Jan Gruber.

Class Instructor Name Date. Classroom Tips Class Roster – Please Sign In Class Roster – Please Sign In Internet Usage Internet Usage –Breaks and Lunch.

The DSpace Course Module – An introduction to DSpace.

Peter J. Briggs, Liz Potterton *, Pryank Patel, Alun Ashton, Charles Ballard, Martyn Winn CLRC Daresbury Laboratory, Warrington, Cheshire WA4 4AD, UK *

28 Mar 06Automation1 Overview of developments within CCP4 Generation 1 ccp4i tasks Generation 2 isolated scripts / web service Generation 3 integrated.

19 th July 2005RUPX Meeting1 Prologue: plan for today General overview of CCP4 (~40-50 minutes) Then (for those who are interested): More technical overview/demo.

Authors Project Database Handler The project database handler dbCCP4i is a small server program that handles interactions between the job database and.

3rd March 2004PR Conferences and Workshops CCP4: PR, Conferences and Workshops Peter Briggs CCP4, CCLRC/Daresbury Laboratory.

Welcome Plans for the day Key milestones progress Requirements for final report Update on communication with social partners Identify any problems &

Markus Dolensky, ESO Technical Lead The AVO Project Overview & Context ASTRO-WISE ((G)A)VO Meeting, Groningen, 06-May-2004 A number of slides are based.

23 rd March 2005CCP4 Annual Developers’ Meeting 1 DL: Releases, Conferences and Other Activities Peter Briggs, CCP4 Daresbury.

Worldwide Protein Data Bank Worldwide Protein Data Bank History of the PDB  1970s  Community discussions about how to establish.

1 st -4 th December st BioXHIT Annual Meeting WorkPackage 5.2: Implementation of Data management and Project Tracking in Structure Solution Peter.

Welcome to the Preparatory Lunch for workshop chairs & rapporteurs, the chair of the plenary panel discussion & the EC representatives to discuss.

Workshop Visualization of Biological Complexes October 11-12, 2003.

R. Keegan 1, J. Bibby 3, C. Ballard 1, E. Krissinel 1, D. Waterman 1, A. Lebedev 1, M. Winn 2, D. Rigden 3 1 Research Complex at Harwell, STFC Rutherford.

17 th October 2005CCP4 Database Meeting (York) CCP4(i)/BIOXHIT Database Project: Scope, Aims, Plans, Status and all that jazz Peter Briggs, Wanjuan Yang.

EVAN Gender Board January 2007 Katrin Schaefer Sarah Elton Katerina Harvati.

Data Integration and Management A PDB Perspective.

Structure database: PDB Tuomas Hätinen. Protein Data Bank A repository for 3-D biological macromolecular structure. It includes proteins, nucleic acids.

Project Database Handler The Project Database Handler dbCCP4i is a brokering application that mediates interactions between the project database and an.

Protein Data Bank: An Introduction Learning to Use the RCSB PDB Portal.

Data Harvesting: automatic extraction of information necessary for the deposition of structures from protein crystallography Martyn Winn CCP4, Daresbury.

Project Database Handler The Project Database Handler is a brokering application that mediates interactions between the project database and the external.

Real World Experiences in Operating a Collaboratory: The Protein Data Bank Helen M. Berman Board of Governors Professor of Chemistry.

17 th October 2005CCP4 Database Meeting York University Database Requirements for CCP4 Projects Monday 17 th October 2005 Abstract Gather information on.

Alessandro Variola MAY 23 rd 2007 POSIPOL WELCOME WELCOME POSIPOL 2007 Goals Alessandro Variola MAY 23 rd 2007 Posipol Welcome.

Project Database Handler The Project Database Handler is a brokering application, which will mediate interactions between the project database and other.

SR Users Meeting 10-11th September 2003 CCP4 Release 5.0 Peter Briggs CCP4/CCLRC Daresbury Laboratory.

Almost at the end … “If you don’t remember anything else, remember this”

AutoDep 4.0 A data deposition and archival system Sameer Velankar.

28 th May 2005CCP4 Workshop ACA 2005 Orlando FL 1 WK04: A Protein Crystallographic Toolbox: The CCP4 Software Suite ACA 2005 Orlando May 28th 2005.

Software automation – What STAB sees as key aims? 1.Brief review of activities and recommendations (so far) 2.Reality checks 3. Things to do…

Planetary Rovers Workshop Organized by: Richard Volpe Mobility and Robotic Systems Jet Propulsion Laboratory.

CCP4 Study Weekend 2013 “Molecular Replacements”

WORKSHOPS AND CONFERENCES Maeri Howard Administrator/Fat Controller.

Peter J. Briggs, Alun Ashton, Charles Ballard, Martyn Winn and Pryank Patel CCLRC Daresbury Laboratory, Warrington, Cheshire WA4 4AD, UK The CCP4 project.

Almost at the end … “If you don’t remember anything else, remember this”

Vision: Increase regional sharing and collaboration in order to expedite the delivery and adoption of energy efficiency. Conduit is brought to you by NEEA.

Talks! Tour GrantStation: Your Fast Track to Funding Audio is only available by calling this number: Conference Call: ; Access Code:

What does the future hold? SAPHIRE CCP4 libraries Program Developments More automation 3D viewer Project CCP4 Study Weekend 2003 BAR!

Project Database Handler The Project Database Handler is a brokering application which will mediate interactions between the project database and other.

CCP4 6.1 and beyond: Tools for Macromolecular Crystallography

Session 4 CEPT Portal, ECC website and other tools

Jmol Training Session Part I: Introduction to the Protein Data Bank

The Protein Data Bank: Evolution of a key resource in biology

Mapping Special Interest Group SNOMED IHTSDO

CCP4 from a user perspective

Project tracking system for the structure solution software pipeline

Almost at the end … “If you don’t remember anything else, remember this !!!!”

Releases, Conferences and Other Activities

CCP4-PDB Workshop ACA 2004 Chicago

Technical Committee Hamid Vakilzadian

Core Activities Review of 06/07 Plans for 07/08 29 Mar 05 Review.

MGA UPDATE Member Geographic Activities IEEE Central Texas Section T

N6: A Protein Crystallographic Toolbox:

Presentation transcript:

23 rd August 2005CCP4-RCSB Workshop IUCr 2005 Florence Italy 1 N6: A Protein Crystallographic Toolbox: The CCP4 Software Suite and RCSB PDB Deposition Tools IUCr 2005 Florence Italy August 23rd

23 rd August 2005CCP4-RCSB Workshop IUCr 2005 Florence Italy 2 About this workshop … The objective of this one-day workshop is not to teach crystallography but to teach people how to use some of the programs distributed with the CCP4 package to do protein crystallography, and how to get the best from the RCSB PDB when they deposit their structures. Thanks to … Maeri Howard & Judy Flippen-Anderson (co-organisers) Helen Berman CCP4 and RCSB PDB The IUCr (Annalisa Guerri) … and all the workshop speakers

23 rd August 2005CCP4-RCSB Workshop IUCr 2005 Florence Italy 3 About CCP4 … CCP4 is the Collaborative Computational Project no.4 UK-based initiative Provides software for Macromolecular X-ray Crystallography Educational remit to promote “good practice” Core funding from BBSRC Additional income from industrial receipts Core staff based at CCLRC Daresbury Laboratory in UK Maintain, develop and release core software Make releases of the software suite Coordinate other activities including: Annual study weekend Newsletters Maintain website, bulletin board, problems pages Conferences, workshops (like this one!)

23 rd August 2005CCP4-RCSB Workshop IUCr 2005 Florence Italy 4 CCP4 funds other staff working on CCP4-related projects and programs across the UK Software is also provided by developers not funded by CCP4 CCP4-related software developments CCP4 Molecular Graphics (CCP4mg, Coot) Refmac5 Mosflm Phaser, Pirate, BP3, Chooch … Other projects CCP4 Automation effort Involvement in various European projects: e-HTPX, SPINE, BIOXHIT, PIMS …

23 rd August 2005CCP4-RCSB Workshop IUCr 2005 Florence Italy 5 Some general CCP4 resources … CCP4 website Links to lots of useful information (downloads, documentation…) Bulletin Board ccp4bb lively forum for discussing all aspects of protein crystallography “Sorry for the non-CCP4 related query…” To (un)subscribe: Newsletters “Journal style” newsletters Current and past issues:

23 rd August 2005CCP4-RCSB Workshop IUCr 2005 Florence Italy 6 The Protein Data Bank is the single worldwide repository for the processing and distribution of 3-D biological macromolecular structure data. The RCSB PDB’s mission is provide the most accurate, well- annotated data in the most timely and efficient way possible to facilitate new discoveries and advances in science. As of August 1, 2005 there are more than 31,500 structures available in the archive.

23 rd August 2005CCP4-RCSB Workshop IUCr 2005 Florence Italy 7 Tools available for deposition and validation ADIT ( deposit.rcsb.org/adit/) pdb_extract ( pdb-extract.rutgers.edu/) also available through CCP4i Ligand Depot (ligand-depot.rutgers.edu/) Validation suite (deposit.rcsb.org/validate/) The RCSB PDB’s new and improved search engine is available for beta testing at pdbbeta.rcsb.org

23 rd August 2005CCP4-RCSB Workshop IUCr 2005 Florence Italy 8 Exhibit Booths CCP4 is at stand 11 Meet CCP4 staff and developers Software demos, questions, manuals wwPDB is at booths wwPDB members are exhibiting jointly at IUCr XX RCSB PDB MSD/EBI PDBj Staff from all three sites will be available Website/software demos Please stop by for a visit!

23 rd August 2005CCP4-RCSB Workshop IUCr 2005 Florence Italy 9 Workshop Timetable 8:30amIntroduction and Welcome Morning session: General 8:45An Introduction to the CCP4 Package: Utilities, Tricks and TipsPeter Briggs 9:30Overview of using CCP4 for PXMartin Noble 10:30Coffee 11:00Data Processing and Reduction using MOSFLM & SCALAGwyndaf Evans 12:30Lunch Afternoon session 13:30TLS Refinement with REFMAC5Martyn Winn 14:30CCP4 Molecular Graphics: Pictures & Movies With CCP4MGLiz Potterton 15:00Coffee 15:30Coot And Graphical Model Building ToolsPaul Emsley 16:00Data Deposition And Validation Using RCSB PDB ToolsKyle Burkhardt Summing Up 16:45 Summary, or: "if you don't remember anything else from today, remember this..." Questions and Answers 17:00 Close

23 rd August 2005CCP4-RCSB Workshop IUCr 2005 Florence Italy 10 Practical points … Coffee breaks at 10:30am and 3:00pm Lunch is provided by the IUCr as part of the workshop fee Packs contain copies of all the talks Please let us know if there are missing documents/other problems There are also questionnaires in the packs – please give us feedback! Speakers Please please please stick to time Mr Timer will assist you … Gather for photo at morning coffee