2019-07-17 : 8665 EMDB map entries, 3614 PDB coordinate entries RCSB PDB | PDBe

EM software

Below is a list of software programs for generation, fitting, and analysis of 3D maps from electron microscopy images. See also: EM software wiki page. Please send corrections/additions to help@emdataresource.org.

Program Type Reference
Link Focus (successor to 2dx) General Package Biyani et al 2017
Link EMBFACTOR Bfactor correction Fernandez et al 2008
Link TomoAlign Image alignment, Tomography Fernandez et al 2018
Link ACE/ACE2 CTF correction Mallick et al 2005
Link ctffind/ctftilt CTF correction Rohou & Grigorieff 2015
Link EMCTF/TOMOCTF CTF correction Fernandez & Crowther 2006
Link Leginon data acquisition Suloway et al 2005
Link UCSF Tomography data acquisition, tomography Zheng et al 2004
Link TOMOAND/TOMOBFLOW denoising Fernandez & Li 2003
Link Bsoft reconstruction Heymann 2018
Link cisTEM reconstruction
Link CryoSPARC reconstruction Punjani et al 2017
Link EMAN/EMAN2 reconstruction Bell et al 2018
Link Eos reconstruction
Link IMAGIC reconstruction
Link IPLT reconstruction Schenk et al 2013
Link CCP-EM reconstruction Burnley et al 2017
Link Simple reconstruction Reboul et al 2018
Link Sparx reconstruction Behrmann et al 2012
Link Spider reconstruction Leith et al 2012
Link Suprim reconstruction
Link SPHIRE reconstruction Moriya et al 2017
Link Xmipp reconstruction de la Rosa-Treví et al 2013
Link IHRSR helical Egelman 2010
Link Phoelix helical
Link Ruby-Helix helical Metlagel et al 2007
Link Spring helical Desfosses et al 2014
Link AUTO3DEM icosahedral Yan et al 2007
Link em2em map conversion
Link ADP_EM modelling Garzon et al 2007
Link UCSF Chimera modelling, visualization Petterson et al 2004
Link COOT modelling, visualization Brown et al 2015
Link DireX modelling Wang & Schroeder 2012
Link EMfit modelling Rossmann et al 2001
Link Flex-EM modelling Joseph et al 2016
Link Gorgon modelling Baker et al 2012
Link iMODFIT modelling Lopéz-Banco & Chacon 2013
Link MDFF modelling Trabuco et al 2009
Link NMFF modelling Tama et al 2004
Link NORMA modelling Suhre et al 2006
Link Phenix modelling Afonine et al 2018
Link REFMAC modelling Brown et al 2015
Link Rosetta for cryoEM modelling Wang et al 2016
Link Situs modelling Kovacs et al 2018
Link TEMPy modelling, model validation Farabella et al 2015
Link VMD modelling, visuallization
Link EMRinger model validation Barad et al 2015
Link Molprobity model validation Williams et al 2018
Link SamViewer particle picking
Link Signature particle picking Chen & Grigorieff 2007
Link FSC resolution estimation
Link rmeasure resolution estimation Sousa & Grigorieff 2007
Link Frealign reconstruction Lyumkis et al 2013
Link PFT3DR reconstruction
Link RELION reconstruction Scheres 2012
Link Dynamo tomography Castano-Diez et al 2012
Link EM3D tomography
Link IMOD tomography Mastronarde & Held 2017
Link protomo tomography Winkler & Taylor 2006
Link SerialEM data acquisition, tomography Mastronarde 2005
Link TOM tomography Nickell et al 2005
Link Amira-Avizo visualization
Link CCP4mg visualization McNicholas et al 2011
Link RIVEM visualization
Link Appion workflow Lander et al 2009
Link Scipion workflow
Link motioncor2 movie frame alignment Zheng et al 2017
Link Gautomatch particle picking
Link Gctf CTF correction
Link ResMap Local Resolution Estimation Kucukelbir et al 2014
Link Unblur/Summovie movie frame alignment Grant & Grigorieff 2015
Link FragFit modelling server Tiemann et al 2018
Link Powerfit modelling server Zundert et al 2017
Link Samuel workflow scripts
Link ASPIRE reconstruction
Link APPLE-Picker particle picking Heimowitz et al 2018
Link Topaz particle picking
CDMD modelling Igaev et al 2019

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