2014-07-23 : 2411 EMDB map entries, 852 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://nramm.scripps.edu/software/ace/
ctffind CTF correction http://emlab.rose2.brandeis.edu/ctf
ctftilt CTF correction http://emlab.rose2.brandeis.edu/ctf
EMCTF CTF correction http://www.ual.es/~jjfdez/SW/emctf.html
TOMOCTF CTF correction http://www.ual.es/~jjfdez/SW/tomoctf.html
Leginon data acquisition http://leginon.scripps.edu/
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
Cyclops General package http://www.bfsc.leidenuniv.nl/software/Cyclops/
EMAN General package http://blake.bcm.edu/EMAN/
Eos General package http://www.yasunaga-lab.bio.kyutech.ac.jp/Eos/
IMAGIC General package http://www.imagescience.de/imagic/index.htm
IPLT General package http://www.iplt.org/wiki
MDPP General package http://gcrc.med.nyu.edu/mdpp/
MRC General package http://www2.mrc-lmb.cam.ac.uk/image2000.html
Additional Documentation: Helical Crystals, 2D Crystals
pyappion General package http://code.google.com/p/appion/
Simple General package http://simple.stanford.edu
Sparx General package http://macro-em.org/sparxwiki/SparxWiki
Spider General package http://www.wadsworth.org/spider_doc/spider/docs/spider.html
Suprim General package http://nramm.scripps.edu/software/suprim/
Xmipp General package http://xmipp.cnb.csic.es/
IHRSR helical scripts available from Ed Egelman
Phoelix helical http://nramm.scripps.edu/software/phoelix/
Ruby-Helix helical http://structure.biophys.kyoto-u.ac.jp/software/software.html
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/
DireX modelling https://simtk.org/home/direx/
EMfit modelling link to Rossmann Lab software
Gorgon modelling http://gorgon.wustl.edu
iMODFIT modelling http://chaconlab.org/methods/fitting/imodfit
NMFF modelling http://mmtsb.org/software/nmff.html
NORMA modelling http://www.elnemo.org/NORMA/
Situs modelling http://situs.biomachina.org/
UROX modelling http://sites.google.com/site/xsiebert/urox
VEDA modelling http://mem.ibs.fr/VEDA
VMD modelling http://www.ks.uiuc.edu/Research/vmd/
YUP.SCX modelling http://rumour.biology.gatech.edu/YammpWeb/userman/yupscx/intro.shtml
Appion Tilt Picker particle selection http://code.google.com/p/appion/
Samviewer particle selection https://sites.google.com/site/maofuliao/samviewer
Signature particle selection http://emlab.rose2.brandeis.edu/signature
SwarmPS particle selection http://www.imb.uq.edu.au/index.html?page=44665
FSC resolution estimation http://www.imagescience.de/fsc/index.htm
rmeasure resolution estimation http://emlab.rose2.brandeis.edu/rmeasure
Segger segmentation http://ncmi.bcm.edu/ncmi/software/segger/
Frealign single particle http://emlab.rose2.brandeis.edu/frealign
PFT2DR single particle http://people.chem.byu.edu/belnap/pft3dr
RELION single particle http://www2.mrc-lmb.cam.ac.uk/relion
Dynamo tomography http://dynamo.bioz.unibas.ch/
EM3D tomography http://em3d.stanford.edu/index.html
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/
Chimera visualization http://www.cgl.ucsf.edu/chimera/
RIVEM visualization link to Rossmann lab software
UROX visualization http://sites.google.com/site/xsiebert/urox
VMD visualization http://www.ks.uiuc.edu/Research/vmd/