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Collaborative Computational Project
for Electron cryo-Microscopy

MRC

CCP-EM Documentation

CCP-EM Mailing List

There is 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.

Computational Carbon Footprint

Green Algorithms is an useful website which estimates the carbon footprint based on runtime, number of GPU & CPUs, memory and location. It also provides guidance on how to minimise carbon usage.

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.

Tutorials and Course Material

General CCP-EM tutorial page

IUCr Satellite workshop - Methods of Structural Biology 2021

Teaching material from the workshop.

S²C² CCP-EM Modelling Workshop, Nov 2020

Teaching material from the workshop.

CCP-EM Icknield Workshop 2019: High resolution model building and refinement for cryoEM

Teaching material from the CCP-EM course hosted at Diamond Light Source and Research Complex at Harwell in April 2019. The material includes presentations, tutorials and example data, for Flex-EM, Refmac, Coot, ARP/wARP, LocScale and Buccaneer.

Refmac CCP-EM Tutorial

Refmac CCP-EM tutorial demostrates automated model refinement using Refmac.

Updated Molrep EM Tutorial

New Molrep tutorial from Alexey Vagin detailing how to use Molrep with EM maps from scripts.

CCP-EM Icknield Workshop 2017: High resolution model building and refinement for cryoEM

Teaching material from the CCP-EM course hosted at Diamond Light Source and Research Complex at Harwell in April 2017. The material includes presentations, tutorials and example data, for Flex-EM, Refmac, Coot and Buccaneer.

Instruct Workshop 2015: 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 2017

Presentations and videos and Scientific Training site, 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 Alexey Vagin detailing how to use Molrep with EM maps.

CCP-EM Logos

Standard logo

Standard logo with white background

Square logo without text

Useful Links

ProjectsSoftwareGuides
3dem mailing list
Royal Microscopical Society
BioImaging UK
Cryo-Microscopy Group
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