2017-12-13 : 5449 EMDB map entries, 1919 PDB coordinate entries PDBe | RCSB    

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EM software

Listed below are software programs used in the generation, analysis, and fitting of 3D maps from electron microscopy images. The starting point for the list was the EM software wiki page. Please send corrections/additions to help@emdatabank.org.

Click on the Program and Type table headers to change the sort order.

ProgramTypeWebSite
2dx 2D crystal http://2dx.org/
EMBFACTOR Bfactor correction http://www.ual.es/~jjfdez/SW/embfactor.html
ACE CTF correction http://emg.nysbc.org/redmine/projects/software/wiki/Software
ctffind CTF correction http://grigoriefflab.janelia.org/ctf
ctftilt CTF correction http://grigoriefflab.janelia.org/ctf
EMCTF CTF correction http://www.ual.es/~jjfdez/SW/emctf.html
Gctf CTF correction https://en.wikibooks.org/w/index.php?title=Software_Tools_For_Molecular_Microscopy&stable=0#Gctf
TOMOCTF CTF correction http://www.ual.es/~jjfdez/SW/tomoctf.html
Leginon data acquisition http://leginon.org/
SerialEM data acquisition http://bio3d.colorado.edu/SerialEM/
UCSF Tomography data acquisition http://www.msg.ucsf.edu/em/EMNEW2/tomography_page.html
TOMOAND denoising http://www.ual.es/~jjfdez/SW/tomoand.html
TOMOBFLOW denoising http://www.ual.es/~jjfdez/SW/tomobflow.html
Bsoft General package http://lsbr.niams.nih.gov/bsoft/bsoft.html
cisTEM General package http://cistem.org/
Cyclops General package http://www.bfsc.leidenuniv.nl/software/Cyclops/
CryoSPARC General package http://cryosparc.com
EMAN General package http://blake.bcm.edu/emanwiki/EMAN2
Eos General package http://www.yasunaga-lab.bio.kyutech.ac.jp/Eos/
IMAGIC General package http://www.imagescience.de/imagic.html
IPLT General package http://www.iplt.org/
MDPP General package https://sourceforge.net/projects/mdpp/
MRC General package http://www.ccpem.ac.uk/download.php
Additional Documentation: Helical Crystals, 2D Crystals
Simple General package http://simplecryoem.com/
Sparx General package http://sparx-em.org
Spider General package http://spider.wadsworth.org
Suprim General package http://emg.nysbc.org/redmine/projects/suprim
SPHIRE General package http://sphire.mpg.de/
Xmipp General package http://xmipp.cnb.csic.es/
IHRSR helical scripts available from Ed Egelman
Phoelix helical http://emg.nysbc.org/redmine/projects/phoelix
Ruby-Helix helical http://structure.m.u-tokyo.ac.jp/English/software/Ruby-Helix-Page/ruby-helix.html
Spring helical http://www.sachse.embl.de/emspring
AUTO3DEM icosahedral http://cryoem.ucsd.edu/programs.shtm
IMIRS icosahedral http://www.eicn.ucla.edu/imirs
em2em map conversion https://www.imagescience.de/em2em.html
ADP_EM modelling http://chaconlab.org/methods/fitting/adpem
Chimera modelling http://www.cgl.ucsf.edu/chimera/
COOT modelling http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/
DireX modelling https://simtk.org/home/direx/
EMfit modelling link to Rossmann Lab software
Flex-EM modelling http://salilab.org/Flex-EM/
Gorgon modelling http://gorgon.wustl.edu
iMODFIT modelling http://chaconlab.org/methods/fitting/imodfit
MDFF modelling http://www.ks.uiuc.edu/Research/vmd/plugins/mdff/
NMFF modelling http://mmtsb.org/software/nmff.html
NORMA modelling http://www.elnemo.org/NORMA/
Phenix modelling https://www.phenix-online.org/documentation/reference/real_space_refine.html
REFMAC modelling http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/
RosettaEM modelling http://dimaiolab.ipd.uw.edu/software/
Situs modelling http://situs.biomachina.org/
TEMPy modelling http://tempy.ismb.lon.ac.uk/
VEDA modelling https://github.com/ggoret/VEDA
VMD modelling http://www.ks.uiuc.edu/Research/vmd/
YUP.SCX modelling http://rumour.biology.gatech.edu/YammpWeb/userman/yupscx/intro.shtml
EMRinger model validation http://fraserlab.com/2015/02/18/EMringer/
Molprobity model validation http://molprobity.biochem.duke.edu/
TEMPy model validation http://tempy.ismb.lon.ac.uk/
Appion Tilt Picker particle selection http://appion.org/
Samviewer particle selection https://sites.google.com/site/maofuliao/samviewer
Signature particle selection http://grigoriefflab.janelia.org/signature
FSC resolution estimation http://www.imagescience.de/fsc.html
rmeasure resolution estimation http://grigoriefflab.janelia.org/rmeasure
Segger segmentation http://ncmi.bcm.edu/ncmi/software/segger/docs
Frealign single particle http://grigoriefflab.janelia.org/frealign
PFT3DR single particle http://cores.utah.edu/pft3dr-package/
RELION single particle http://www2.mrc-lmb.cam.ac.uk/relion
Dynamo tomography http://wiki.dynamo.biozentrum.unibas.ch
EM3D tomography http://em3d.stanford.edu/
Ettention tomography http://www.ettention.org
IMOD tomography http://bio3d.colorado.edu/imod/
protomo tomography http://www.electrontomography.org/
SerialEM tomography http://bio3d.colorado.edu/SerialEM/
TOM tomography http://www.biochem.mpg.de/tom/
amira visualization http://www.amira.com/
CCP4mg visualization http://www.ccp4.ac.uk/MG/
Chimera visualization http://www.cgl.ucsf.edu/chimera/
COOT visualization http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/
RIVEM visualization link to Rossmann lab software
VMD visualization http://www.ks.uiuc.edu/Research/vmd/
Appion workflow http://appion.org/
Scipion workflow http://scipion.cnb.csic.es/