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Last Modified: Friday, 11-Oct-2019 08:30:19 EDT

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. There are several Yale facilities offering cryo-EM services.

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.

For the Science Hill Cryo-EM facility, the current data directory is directly accessible from Core workstations in the directory


In the case of the School of Medicine EM facility, the current data directory for the T12 is directly accessible from Core workstations by going to the directory

cd /srv/T12_User_Images

For data access to the West Campus Cryo-EM facility, contact the center's staff.

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

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.

ChimeraX : a "next-generation" Chimera with new features, still under heavy development

cisTEM : process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them

CryoEF : An open-source software package for robust analysis of the orientation distribution of cryoelectron microscopy data.

CryoSPARC : processing for single-particle cryo-EM data
NB: Not available via 'setup' command; access via http://cryocrunch.csb.yale.internal:39000 (from internal network only)

CTFFIND : determination of contrast transfer functions for electron micrographs

em2em : Program to convert images (2-D images and 3-D volumes) from/to formats typically used in 3-D electron microscopy

EMAN2 : EM data processing for particle reconstruction

Gctf : real-time contrast transfer function determination and correction

IMOD : image processing, modeling and display programs used for tomographic reconstruction

MotionCor2 : Correction of electron beam-induced sample motion

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

: 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

THUNDER : particle-filter framework for robust cryoEM 3D reconstruction

Tomviz : a cross platform, open source application for the processing, visualization, and analysis of 3D tomographic data.

Last Modified: Friday, 11-Oct-2019 08:30:19 EDT

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