EMAN2: an extensible image processing suite for electron microscopy.
Citations
4,554 citations
Cites background or methods from "EMAN2: an extensible image processi..."
...Efforts to do so in APPION (Lander et al., 2009) and EMAN2 (Tang et al., 2007) are currently ongoing (personal communication with Bridget Carragher and Steven Ludtke, respectively)....
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..., 2009) and EMAN2 (Tang et al., 2007) are currently ongoing (personal communication with Bridget Carragher and Steven Ludtke, respectively)....
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...Second, general refinement behaviour and computational costs of the MAP optimization approach were tested using an experimental cryo-EM data set of 5168 GroEL particles that is distributed as part of a workshop on the EMAN2 software package (Tang et al., 2007)....
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3,520 citations
Cites methods from "EMAN2: an extensible image processi..."
...In the mean time, also general-purpose programs that already existed, like EMAN2 (Tang et al., 2007), Frealign (Grigorieff, 2007) or IMAGIC (van Heel et al., 1996), were further improved and used for high-resolution structure determination....
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2,919 citations
Cites background or methods from "EMAN2: an extensible image processi..."
...CTF parameters from the text log file can also be easily extracted and used for other programs such as Frealign (Grigorieff, 2007), EMAN (Ludtke et al., 1999; Tang et al., 2007), Spider (Shaikh et al....
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...There are currently several programs available for CTF determination (Ludtke et al., 1999; Mallick et al., 2005; Mindell and Grigorieff, 2003; Penczek et al., 2014; Shaikh et al., 2008; Sorzano et al., 2004; Tang et al., 2007; Vargas et al., 2013; Voortman et al., 2011)....
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...CTF parameters from the text log file can also be easily extracted and used for other programs such as Frealign (Grigorieff, 2007), EMAN (Ludtke et al., 1999; Tang et al., 2007), Spider (Shaikh et al., 2008) and Xmipp (Sorzano et al., 2004) etc....
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1,567 citations
1,034 citations
References
35,698 citations
"EMAN2: an extensible image processi..." refers methods in this paper
...For structural biology, this largely began with the visualization community, Wrst with packages like Chimera (Pettersen et al., 2004), Vision (Sanner et al....
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...For structural biology, this largely began with the visualization community, Wrst with packages like Chimera (Pettersen et al., 2004), Vision (Sanner et al., 2002) and Pymol (http://pymol.sourceforge.net) which are written largely in Python with supporting libraries in C/C++....
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22,762 citations
"EMAN2: an extensible image processi..." refers methods in this paper
...Internally, this infrastructure is implemented using several now-standard C++ programming design patterns (Gamma et al., 1995): Abstract Factories, Factory Methods and Singleton Classes....
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4,830 citations
"EMAN2: an extensible image processi..." refers background or methods in this paper
...Over the last three decades, a wide range of scientiWc image processing packages have been developed for use with electron microscopy, including SPIDER (Frank et al., 1996), IMAGIC (van Heel et al., 1996), BSOFT (Heymann, 2001), FREALIGN (GrigorieV, 1998), EM (Hegerl, 1996), IMIRS (Liang et al., 2002), SUPRIM (Schroeter and Bretaudiere, 1996), IMOD (Kremer et al., 1996), PHOELIX (Carragher et al., 1996), PFT (Baker and Cheng, 1996), the MRC reconstruction tools (Crowther et al., 1996) and Xmipp (Sorzano et al., 2004)....
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..., 2002), SUPRIM (Schroeter and Bretaudiere, 1996), IMOD (Kremer et al., 1996), PHOELIX (Carragher et al....
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...…BSOFT (Heymann, 2001), FREALIGN (GrigorieV, 1998), EM (Hegerl, 1996), IMIRS (Liang et al., 2002), SUPRIM (Schroeter and Bretaudiere, 1996), IMOD (Kremer et al., 1996), PHOELIX (Carragher et al., 1996), PFT (Baker and Cheng, 1996), the MRC reconstruction tools (Crowther et al., 1996) and Xmipp…...
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4,201 citations
"EMAN2: an extensible image processi..." refers methods in this paper
...When we began to work with the PHENIX (Adams et al., 2004, 2002) project to produce SPARX (see the companion piece in this issue), it became clear that many features necessary to take the next steps towards higher resolution reconstructions and development of novel techniques could not be reasonably incorporated into the original EMAN1 design....
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...PHENIX is based on the WxPython toolkit, while EMAN1 makes use of the QT toolkit in C++....
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...When we began to work with the PHE-NIX ( Adams et al., 2004, 2002 ) project to produce SPARX (see the companion piece in this issue), it became clear that many features necessary to take the next steps towards higher resolution reconstructions and development of novel techniques could not be reasonably incorporated into the original EMAN1 design....
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...Current EMAN2 image display widgets use WxPython for PHENIX compatibility....
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...When we began to work with the PHENIX (Adams et al., 2004, 2002) project to produce SPARX (see the companion piece in this issue), it became clear that many features necessary to take the next steps towards higher resolution reconstructions and development of novel techniques could not be…...
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2,570 citations
"EMAN2: an extensible image processi..." refers background in this paper
...This separation opens the possibility of supporting other parallel computing environments like Condor (Litzkow et al., 1988) or systems similar to FoldingAtHome (Shirts and Pande, 2006) in the future, without any substantial internal changes....
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