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Last Modified: Thursday, 09-Mar-2017 11:02:46 EST

Cryo-EM Applications in the CSB Core


Cryo-electron microscopy is a developing alternative to X-ray crystallography for 3-D structure determination. The applications below are some of the more commonly-used programs. See the Core system administrator if other programs are required.

Note that the Core is not involved in the actual sample preparation or data collection process. The first step when using Core resources is making your data locally accessible. It is usually possible to attach a portable drive to Core workstations and using

mount /local/disk1

etc., to access the contents. Remember to use

umount /local/disk1

etc, to safely remove the drive.

In the case of the Electron Microscopy Facility at the Yale School of Medicine, the current temporary data directory is directly accessible from Core workstations by going to the directory /srv/T12_User_Images. I.e.,

cd /srv/T12_User_Images

etc. Note that this folder's contents are generally read-only, so you will probably want to transfer your data to a local external drive or to /srv/frames.

The Bass cryo-EM facility currently under construction will have its own filesharing process, probably similar to the above for the existing facility.


Several of the programs below either run on the command line, or have portions that can optionally do so. In such cases, it might be worth looking into using the batch queue system, especially the "cryo" queue that runs on the multi-GPU system.


Chimera : highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles.

CryoSPARC : processing for single-particle cryo-EM data
NB: Not available via 'setup' command; access via http://cryocrunch.csb.yale.internal:38000 (from internal network only)

CTFFIND : determination of contrast transfer functions for electron micrographs

EMAN2 : EM data processing for particle reconstruction

Gctf : real-time contrast transfer function determination and correction

MotionCor2 : Correction of electron beam-induced sample motion

RELION : Refinement of 3D reconstructions or 2D class averages

ResMap
: Python application w/ GUI for computing local resolution of 3D density maps (integrates with Chimera)

Scipion : EM image processing framework for obtaining 3D models

SPIDER : Image-processing system for EM

Last Modified: Thursday, 09-Mar-2017 11:02:46 EST


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