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Icknield high resolution model building and validation workshop - Icknield V 2019 -
Icknield high resolution model building and validation workshop
- Icknield V 2019 -
First things first...
Where are we...
...why are we here
Collaborative Computational Project for Electron cryo-Microscopy
Support users and developers in computational aspects of biological EM
1. Build UK EM community2. Support software users3. Support developers
Hosted by STFCFunded by MRC & Wellcome Trust
Science & Technology Facilities Council
Located at Research Complex at Harwell, Oxfordshire, UK
Alongside CCP4 core team – shared expertise between projects
CCP-EM & CCP4 | RCaH
eBIC | DLS
TomBurnley
ColinPalmer
MartynWinn
CCP-EM Version 1.3
AgnelJoseph
JolaMirecka
CCP-EM: Model building pipeline
<4Å
Map Model
Buccaneer
Flex-EM
Molrep Refmac
Yes
No
Coot
Docking / Model Building
AutomatedRefinement
InteractiveRefinement
Chimera
Map Optimisation
Mrc to Mtz
LocScale
Dock-EM
sharpen... build… refine… validate... repeat…
sharpen... build… refine… validate... repeat…
ArjenJakobi
LocScale
● Reference-based density scaling for local sharpening of cryo-EM maps
sharpen... build… refine… validate... repeat…
Buccaneer & Nautilus
● Automated model building of protein and nucleic acids
KevinCowtan
Scott Hoh
Find positions Grow fragments
Join
Link RebuildPrune
sharpen... build… refine… validate... repeat…
ARP/wARP
● Automated protein model building and refinement
Grzegorz Chojnowski
sharpen... build… refine… validate... repeat…
Refmac / ProSMART / EDMA
● Automated high resolution refinement
GaribMurshudov
Rob Nicholls
Rangana Warshamanage
sharpen... build… refine… validate... repeat…
Flex-EM / TEMPy
● MD refinement and validation tools
SonyMalhotra
AgnelJoseph
sharpen... build… refine… validate... repeat…
MolProbity
● Atomic structure validation
JaneRichardson
sharpen... build… refine… validate... repeat…
sharpen... build… refine… validate... repeat…
Coot● Molecular graphics tool for
interactive refinement and validation of models
PaulEmsley
AnaCasañal
Judit Debreczeni
sharpen... build… refine… validate... repeat…
ISODLE● Molecular graphics combined with
MD for interactive model building
TristanCroll
….deposit
Osman SalihEBIEMDBEMPIAR
….deposit
kaizen...
...use metrics wisely...
...sometimes there is no right answer
Pavel Afonine
> cp ~/Downloads/ccpem-1.0.0-macosx-x86_64.tar.gz .> tar xvf ccpem-1.0.0-macosx-x86_64.tar.gz> cd ccpem-1.0.0> ./install_ccpem.sh> source setup_ccpem.sh> ccpem
> module load EM/ccpem> ccpem
See cheat sheet-
REMEMBER TO TAKE YOUR DATA HOME!
JoshuaLobo
Acknowledgements
● CCP-EM core team○ Colin Palmer○ Martyn Winn○ Agnel Joseph
● CCP4 core team● DLS / eBIC
○ Alun Ashton○ Mark Basham○ Peijun Zhang
● Birkbeck○ Maya Topf○ Agnel Joseph
● University of Manchester○ Alan Roseman
● EBI○ Gerard Kleywegt○ Ardan Patwardhan
● MRC-LMB○ Garib Murshudov○ Sjors Scheres○ Paul Emsley
● University of York○ Kevin Cowtan○ Soon Wen ‘Scott’ Hoh○ Jon Agirre
● Delft TU○ Arjen Jakobi
Contact details
Website: www.ccpem.ac.uk
Mailing list: www.jiscmail.ac.uk/ccpem
Twitter: @ccp_em
Email us: [email protected]
References:
Collaborative Computational Project for Electron cryo-Microscopy. Acta Cryst. D71, 123-126, 2015
Recent developments in the CCP-EM software suite. Acta Cryst. D73, 469-477, 2017
