Collaborative Computational Project
for Electron cryo-Microscopy

MRC

CCP-EM documentation

CCP-EM mailing list

There is now a mailing list for CCP-EM (supported by JISCMail). The home page for the list is at https://www.jiscmail.ac.uk/CCPEM. To subscribe to the list, click on "Subscribe or Unsubscribe" on this page. Once you have an account, you can manage your list preference from this page. You can also search the CCP-EM archive from here.

The CCP-EM mailing list is primarily intended to support the UK community, though it is open to all. It is not intended to replace 3dem or individual software lists. In addition to general questions, it will also act as the help list for some UK-based software e.g. Sjors Scheres has said that this is the home for Relion questions.

General guides and information

MRC/CCP4 file format
We have agreed an update to the MRC/CCP4 format, called MRC2014. Details of the changes have been published in Cheng et al. (2015) "MRC2014: Extensions to the MRC format header for electron cryo-microscopy and tomography" J. Struct. Biol. 192, 146-150. See separate page for further details.
Euler angle conventions
Some background notes together with links to program-specific documentation.
Linux help
A quick guide to basic Linux commands. Also a slightly longer guide to Linux and vi.

Course Material

Instruct Workshop: Computational tools for combining atomic and volume data

Teaching material from the Instruct course hosted by CCP-EM at Diamond Light Source and Research Complex at Harwell in April 2015. The material includes presentations, tutorials and example data, for Flex-EM, ShapEM/DockEM, CCP4MG, Refmac, Coot, SMaSB/PDBeShape and EMDB.

LMB EM-course 2014

Presentations and videos covering the theoretical basis of modern cryo-EM structure determination.

Caltech EM course

14.5 hours of lecture videos from Prof. Grant Jensen at Caltech/HHMI covering most aspects of cryo-EM.

Molrep CCP4 EM Tutorial

CCP4 Molrep tutorial from Alexei Vagin detailing how to use Molrep with EM maps.

Useful links

ProjectsSoftwareGuides
3dem mailing list
Royal Microscopical Society
BioImaging UK
EMPIAR: pilot image archive for EM
RIBFIND server: finding rigid bodies in protein structures
CryoEM in the Cloud: Amazon instances for cryoEM
A Primer to Single-Particle Cryo-Electron Microscopy, Cheng et al. (2015)
Detailed review of cryoEM, from Elena Orlova and Helen Saibil
Point group symmetries, from Marin van Heel