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Principles & Protocols

Single Particle

• For single particle projects, we are using two packages: SPIDER and EMAN
• In general, EMAN is easier to use and get started with, while SPIDER is more flexible but requires knowledge of its scripting language
• Both packages do the same thing, but you have more control over what happens in SPIDER
• EMAN has a very useful program, boxer, which we use to box particles
• Other available packages include IMAGIC ($), Xmipp (compatable with SPIDER), EMAN2/SPARX (very new),

Tomography

• We are using two software packages for data processing, protomo and IMOD
• IMOD has a graphical user interface and can be picked up fairly easily
• IMOD requires fiducial markers for a good reconstruction
• protomo works without fiducial markers, but has a command line interface for most tasks

2d Crystallography

• We have the MRC suite of software for processing 2d crystals
• We also have 2DX, a graphical user interface which uses the MRC package

Helical

• We are using our adaptions to Nigel Unwin's software
• This software is a little difficult to learn and use, but staff assistance is available

-- BillRice - 10 Aug 2009