Erice2010:workshop2
This is the detailed information for workshop #2, CCP4 by Murshudov, Erice 2010.
Aim
Tutors:
- Garib Murshudov
The aim of this workshop is to introduce some of the newer CCP4 software particularly:
Buccaneer - automated model building
CCP4mg - presentation graphics
The workshop will be split roughly into two tutorials:
- Building a model into a marginal electron density map obtained from SIRAS phasing using Buccaneer, and examining the model in Coot. The tutorial will also cover phase improvement using DM and simple refinement using Refmac
- Presentation graphics using CCP4mg, and a selection of model analysis tools such as SSM and PISA.
In the time available, we are not able to cover all aspects of CCP4. If you have a particular interest or questions on other CCP4 software we will do our best to help - emailing us before the meeting may help!
For contact information, see the individual tutor pages, linked above.
Suitability
This workshop is suitable for complete novices. However, it would be useful to know beforehand how many students have general experience in solving structures via protein crystallography, and specifically how many have used ccp4 programs and ccp4i. If you are an expert, then please contact us with your interests, and we can perhaps arrange for separate discussions during the meeting.
Materials
The following articles give some background information on the programs used:
- Cowtan, K. "Fitting molecular fragments into electron density" Acta Cryst. D64, 83-89 (2008)
- Emsley, P. and Cowtan, K. "Coot: model-building tools for molecular graphics" Acta Cryst. D60, 2126-2132 (2004)
- Potterton E, McNicholas S, Krissinel E, Cowtan K, Noble M "The CCP4 molecular-graphics project" Acta Cryst. D58, 1955-1957 (2002)
See also the following CCP4 Newsletter articles
- Summer 2007 article 7 "New Features in Coot", Paul Emsley
- Summer 2007 article 8 "CCP4mg:The Picture Wizard", Liz Potterton and Stuart McNicholas
- Summer 2006 article 5 "The Buccaneer protein model building software" Kevin Cowtan
Finally, see the new CCP4 wiki and especially the following pages:
- Phase improvement with DM
- Phase improvement by NCS averaging with DM
- Automated model building with Buccaneer
Protocol
For presentation molecular graphics using CCP4mg you can work on the introductory tutorials from
http://www.ysbl.york.ac.uk/~ccp4mg/ccp4mg_help/tutorial/index.html
and then choose the tutorials that interest you. Better still bring your own data and/or ideas for pictures or movies to try out.
The model building tutorial takes the form of an example dataset, for which initial experimental phases are given, together with a short worksheet outlining the problem and the steps to be taken. More details on running the programs are given on the CCP4 wiki and you are referred to the appropriate section there.
The example data and worksheet will be available here soon.
Extras
We have some extra tutorials in case you finish the workshop early, but if you do the set tutorials thoroughly then you shouldn't have much spare time!