# Software Tools For Molecular Microscopy/Application tools

Packages that offer a tool or a set of tools to permit the analysis of data in one or more class of structural problems. These have generally been developed to manage one specific step in the structural analysis, for example CTF correction, particle picking etc.

## Data Acquisition
#### Leginon

    Website: http://leginon.scripps.edu Current version: 2.0 Contact: amisoftware@scripps.edu Leginon is a system designed for automated collection of images from a transmission electron microscope. Instruments supported: FEI Tecnai series TEM, Tietz and Gatan CCD cameras. On August 1, 2007, Leginon 1.4 was released as open source. Support: Operating systems: Linux/Windows Image format support: MRC Cost: Free/Open source, Apache 2.0 Primary Publication to Cite: Suloway C, Pulokas J, Fellmann D; et al. (2005). "Automated molecular microscopy: the new Leginon system". J. Struct. Biol. 151 (1): 41–60. doi:10.1016/j.jsb.2005.03.010. PMID 15890530. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link) Additional References: Suloway C, Shi J, Cheng A; et al. (2009). "Fully automated, sequential tilt-series acquisition with Leginon". J. Struct. Biol. 167 (1): 11–8. doi:10.1016/j.jsb.2009.03.019. PMC 2724967. PMID 19361558. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link) Stagg SM, Lander GC, Pulokas J; et al. (2006). "Automated cryoEM data acquisition and analysis of 284742 particles of GroEL". J. Struct. Biol. 155 (3): 470–81. doi:10.1016/j.jsb.2006.04.005. PMID 16762565. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link) Yoshioka C, Pulokas J, Fellmann D, Potter CS, Milligan RA, Carragher B (2007). "Automation of random conical tilt and orthogonal tilt data collection using feature-based correlation". J. Struct. Biol. 159 (3): 335–46. doi:10.1016/j.jsb.2007.03.005. PMC 2043090. PMID 17524663. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link) Cheng A, Leung A, Fellmann D; et al. (2007). "Towards automated screening of two-dimensional crystals". J. Struct. Biol. 160 (3): 324–31. doi:10.1016/j.jsb.2007.09.012. PMC 2141647. PMID 17977016. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)

### SerialEM

    see Software_Tools_For_Molecular_Microscopy/Specific_packages#SerialEM

### UCSF Tomography

    see Software_Tools_For_Molecular_Microscopy/Specific_packages#UCSF_Tomography

### TOM Toolbox

    see Software_Tools_For_Molecular_Microscopy/Specific_packages#TOM_Toolbox

## Particle Selection
#### DoG Picker

    Website: http://ami.scripps.edu/redmine/projects/ami/wiki/DoGpicker Current version: 0.2 Contact: appion@scripps.edu DoG Picker is a simple particle picker that picks particles that resemble a blob using the Difference of Gaussians algorithm. It is intergrated into the TiltPicker program (below), Support: Operating systems: Unix Image format support: MRC Cost: Free/Open source, Apache License v2.0 Written In: Python Primary Publication to Cite: Voss NR, Yoshioka CK, Radermacher M, Potter CS, Carragher B (2009). "DoG Picker and TiltPicker: software tools to facilitate particle selection in single particle electron microscopy". J. Struct. Biol. 166 (2): 205–13. doi:10.1016/j.jsb.2009.01.004. PMC 2768396. PMID 19374019. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)

#### FindEM

    Website: http://ami.scripps.edu/redmine/projects/ami/wiki/FindEM Current version: 2.0 Contact: appion@scripps.edu The FindEM program is based on projection matching using local real-space correlation with a series of templates. Real-space algorithms are traditionally relatively slow, but a fast Fourier based implementation of the real-space local correlation function has been introduced which is approximately two orders of magnitude faster for the projection matching application. This algorithm is referred to as the “Fast Local Correlation Function” or FLCF. Support: Operating systems: Unix Image format support: MRC Cost: Free/Open source Primary Publication to Cite: Roseman, A.M. (2004). "FindEM—a fast, efficient program for automatic selection of particles from electron micrographs". Journal of Structural Biology. 145 (1–2): 91–99. doi:10.1016/j.jsb.2003.11.007. PMID 15065677. Additional References: Roseman, A.M. (2003). "Particle finding in electron micrographs using a fast local correlation algorithm". Ultramicroscopy. 94 (3–4): 225–236. PMID 12524193.

#### Signature

    Website: http://emlab.rose2.brandeis.edu Contact: niko @brandeis.edu A particle selection system for molecular electron microscopy. It applies a hierarchical screening procedure to identify molecular particles in EM micrographs. The user interface of the program provides versatile functions to facilitate image data visualization, particle annotation and particle quality inspection. The system design emphasizes both functionality and usability. Support: Operating systems: Linux, Mac OS X, MS Windows Image format support: MRC, TIFF Cost: Free/Open Source, GPL Primary Publication to Cite: Chen, J. Z. (2007). "SIGNATURE: A single-particle selection system for molecular electron microscopy". Journal of Structural Biology. 157: 168–173. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)

#### SwarmPS

    Website: http://www.imb.uq.edu.au/swarmps Current version: 0.9.2 Contact: d.woolford @imb.uq.edu.au A specialised graphical user interface designed to streamline the process of particle selection from electron micrograph data sets. It provides implementations of both template matching and edge detection algorithms, has an intuitive and easy to use interface, and can be used to obtain useful results on most data sets that are generated in electron microscopy. Currently users can expect to select about 1000-4000 particles per hour of interaction. Support: Operating systems: Linux Image format support: Most image formats Cost: Free for academic use under a software license agreement Primary Publication to Cite: Woolford, D. (2007). "SwarmPS: Rapid, semi-automated single particle selection software". Journal of Structural Biology. 157: 174–188. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)

#### TiltPicker

    Website: http://ami.scripps.edu/redmine/projects/ami/wiki/TiltPicker Current version: 2.0 Contact: vossman77@yahoo.com A graphical user interface for picking particles from image tilt pairs for such applications as random conical tilt (RCT) and orthogonal tilt reconstruction (OTR). TiltPicker borrows its interface from Leginon and re-implements many of the tilt picking features of SPIDER WEB that can be run on modern computers. Support: Operating systems: Linux, Mac OS X, Windows, other Unices Image format support: Cost: Free/Open Source, Apache v2.0 Primary Publication to Cite: Voss NR, Yoshioka CK, Radermacher M, Potter CS, Carragher B (2009). "DoG Picker and TiltPicker: software tools to facilitate particle selection in single particle electron microscopy". J. Struct. Biol. 166 (2): 205–13. doi:10.1016/j.jsb.2009.01.004. PMC 2768396. PMID 19374019. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)

#### TMaCS

    Website: https://sites.google.com/site/rubinsteingroup/particle-selection Current version: 1.0 Contact: john.rubinstein@utoronto.ca, jianhua.zhao@utoronto.ca Template Matching and Classification System. Template matching identifies candidate particle images while a Support Vector Machine algorithm is interactively trained to distinguish particles from non-particles. Support: Operating systems: Linux Image format support: MRC Cost: Free/Open Source Primary Publication to Cite: Zhao J, Brubaker MA, Rubinstein JL (2013). "TMaCS: A hybrid template matching and classification system for automated particle selection". J. Struct. Biol. In Press. {{cite journal}}: Cite has empty unknown parameter: |month= (help)CS1 maint: multiple names: authors list (link)

## CTF Estimation and Correction
#### ACE

    Website: http://ami.scripps.edu/redmine/projects/ami/wiki/ACE Current version: 2.3.1 Contact: amisoftware@scripps.edu A completely automated algorithm for estimating the parameters of the contrast transfer function (CTF) of a transmission electron microscope. A MATLAB implementation of the algorithm, called ACE, is freely available. See also author's website: http://graphics.ucsd.edu/~spmallick/research/ace/index.html Support: Operating systems: MATLAB Image format support: MRC Cost: Free/Open Source, Apache License v2.0 Written In: MATLAB Primary Publication to Cite: Mallick, S.P. (2005). "ACE: Automated CTF Estimation". Ultramicroscopy. 104 (1): 8–29. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)

#### ACE2

    Website: http://ami.scripps.edu/redmine/projects/ami/wiki/ACE2 Current version: 2.0 Contact: appion@scripps.edu ACE2 is CTF estimation and correction program using the algorithms developed by Satya et al. (see ACE) rewritten in Objective-C programming language and does not require MATLAB. Support: Operating systems: Unix (specifically, Mac OS X and Linux) Image format support: MRC Cost: Free/Open source, Apache License v2.0 Written In: Objective-C Primary Publication to Cite: Unpublished

#### CTFfind3 and CTFtilt

    Website: http://emlab.rose2.brandeis.edu/ Current version: 3.3 and 1.4 Contact: niko [at] brandeis.edu Programs for finding CTFs of electron micrographs Support: Operating systems: Linux, IRIX, OSF Image format support: MRC Cost: Free/Open Source, GPL Written In: Fortran Primary Publication to Cite: Mindell, J.A. (2003). "Accurate determination of local defocus and specimen tilt in electron microscopy". Journal of Structural Biology. 142: 334–347. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)

#### ctf Explorer

    Website: http://www.maxsidorov.com/ctfexplorer/index.htm Current version: 0.999a Contact: Maxim V. Sidorov, mathebuilder [at] gmail.com allows to calculate the Phase Contrast Transfer Function (CTF): a useful characteristics in Electron Microscopy Support: Operating systems: Windows 95/98/NT4/2000/XP Image format support: Cost: , w:Postcardware, freeware Primary Publication to Cite: Sidorov, Max V. (2002). "ctfExplorer: Interactive Software for 1d and 2d Calculation and Visualization Of TEM Phase Contrast Transfer Function". 8 (S02): 1572CD–1573CD. doi:10.1017.S1431927602104442. {{cite journal}}: Cite journal requires |journal= (help); Check |doi= value (help); Cite has empty unknown parameter: |pmcid= (help)

#### EMCTF

    Website: http://sites.google.com/site/3demimageprocessing/emctf Current version: 1.1 Contact: jjfernandez.software at gmail.com CTF determination of non-astigmatic images in electron cryomicroscopy Support: Operating systems: Linux, Mac OS X Image format support: MRC Cost: Free for academic users Primary Publication to Cite: Fernandez, J.J. (2006). "CTF determination and correction in electron cryotomography". Ultramicroscopy. 106: 587–596. doi:10.1016/j.ultramic.2006.02.004. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help) Additional References: Fernandez, J.J. (1997). "A spectral estimation approach to contrast transfer function detection in electron microscopy". Ultramicroscopy. 68: 267–295. doi:10.1016/S0304-3991(97)00032-6. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)

#### TOMOCTF

    Website: http://sites.google.com/site/3demimageprocessing/tomoctf Current version: 1.1 (October 2012) Contact: jjfernandez.software at gmail.com CTF determination and correction in electron tomography Support: Operating systems: Linux, Mac OS X Image format support: MRC Cost: Free for academic users Primary Publication to Cite: Fernandez, J.J. (2006). "CTF determination and correction in electron cryotomography". Ultramicroscopy. 106: 587–596. doi:10.1016/j.ultramic.2006.02.004. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)

#### fitctf

    Website: http://ncmi.bcm.edu/software/fitctf Contact: CYang@lbl.gov Estimating contrast transfer function and associated parameters by constrained non-linear optimization Support: Operating systems: Linux, Windows, and Mac OS X Image format support: MRC Cost: free Primary Publication to Cite: Yang, C (2009). "Estimating contrast transfer function and associated parameters by constrained non-linear optimization". Journal of Microscopy. 233 (3): 391–403. doi:10.1111/j.1365-2818.2009.03137.x. PMID 19250460. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)

#### FitCTF2

    Website: http://jiang.bio.purdue.edu/software.php Contact: jiang12@purdue.edu A graph theory method for determination of cryo-EM image focuses Support: Operating systems: Linux Image format support: MRC Cost: Free for academic users Written In: Python Primary Publication to Cite: Jiang, Wen (2012). "A graph theory method for determination of cryo-EM image focuses". Journal of Structural Biology. 180 (2): 343–351. doi:10.1016/j.jsb.2012.07.005. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)

## 3D Reconstruction
#### TOMO3D

    Website: http://sites.google.com/site/3demimageprocessing/tomo3d Current version: 1.3.4 (April 2012) Contact: jjfernandez.software at gmail.com Fast tomographic reconstruction on standard multicore computers with WBP and SIRT. Support: Operating systems: Linux, Mac OS X, Windows Image format support: MRC Cost: Free for academic users Primary Publication to Cite: Agulleiro, J.I. (2011). "Fast tomographic reconstruction on multicore computers". Bioinformatics. 27: 582–583. doi:10.1093/bioinformatics/btq692. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help) Additional References: Agulleiro, J.I. (2010). "Vectorization with SIMD extensions speeds up reconstruction in electron tomography". Journal of Structural Biology. 170: 570–575. doi:10.1016/j.jsb.2010.01.008. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help) Agulleiro, J.I. (2012). "Evaluation of a multicore-optimized implementation for tomographic reconstruction". PLoS ONE. 7 (11): e48261. doi:10.1371/journal.pone.0048261. PMID 23139768. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)

#### TOMO3Dhybrid

    Website: http://sites.google.com/site/3demimageprocessing/tomo3dhybrid Current version: 1.0 (February 2012) Contact: jjfernandez.software at gmail.com Fast tomographic reconstruction (WBP,SIRT) with CPU+GPU co-processing Support: Operating systems: Linux Image format support: MRC Cost: Free for academic users Primary Publication to Cite: Agulleiro, J.I. (2012). "Hybrid computing: CPU+GPU co-processing and its application to tomographic reconstruction". Ultramicroscopy. 115: 109–114. doi:10.1016/j.ultramic.2012.02.003. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)

## Resolution Estimation
#### FSC

    Website: http://imagescience.de/fsc/ Contact: michael @ImageScience.de Program to calculate the Fourier Shell Correlation of two 3D volumes. The three-dimensional Fourier Shell Correlation (FSC) measures the normalised cross correlation coefficient between two 3D volumes over corresponding shells in Fourier space, i.e., as a function of spatial frequency. The (modified) 3-sigma criterion indicates where the FSC systematically emerges above the expected random correlations of the background noise. The 1/2-bit information threshold criteria express where we have already collected a sufficient amount of data in the final 3D reconstruction to allow a direct structural interpretation at that resolution level. The 1/2-bit curve is calibrated to approximately yield resolution values comparable to resolution values in use in X-ray crystallography (FOM). Support: Operating systems: Linux/Unix, Mac OS X (Intel), MS Windows Image format support: IMAGIC, Spider, CCP4, MRC, TIFF, etc. Cost: Free Primary Publication to Cite: Harauz, G. (1986). "Exact filters for general geometry three dimensional reconstruction". Optik. 78: 146–156. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help) Additional References: van Heel, M. (2005). "Fourier shell correlation threshold criteria". Journal of Structural Biology. 151: 250–262. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)

#### RMEASURE

    Website: http://emlab.rose2.brandeis.edu/ Current version: 1.05 Contact: niko @brandeis.edu A computational method that allows the measurement of the signal-to-noise ratio and resolution of a three-dimensional structure obtained by single particle electron microscopy and reconstruction. The method does not rely on the availability of the original image data or the calculation of several structures from different parts of the data that are needed for the commonly used Fourier Shell Correlation criterion. Instead, the correlation between neighboring Fourier pixels is calculated and used to distinguish signal from noise. Support: Operating systems: Linux, IRIX, OSF, Mac OS X Image format support: MRC, Spider Cost: Free/Open Source, GPL Primary Publication to Cite: Sousa, D. (2007). "Ab initio resolution measurement for single particle structures". Journal of Structural Biology. 157: 201–210. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)

## Denoising
#### iMed

    Website: http://coan.burnham.org Contact: coan@burnham.org Software for automatic noise reduction using iterative median filtering. Support: Operating systems: Linux Image format support: MRC Cost: Free for academic users Primary Publication to Cite: van der Heide P, Xu XP, Marsh BJ, Hanein D, Volkmann N (2007). "Efficient automatic noise reduction of electron tomographic reconstructions based on iterative median filtering". J. Struct. Biol. 158: 196–204. PMID 17224280. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help)CS1 maint: multiple names: authors list (link)

#### TOMOAND

    Website: http://sites.google.com/site/3demimageprocessing/tomoand Current version: 2.0 (September 2011) Contact: jjfernandez.software at gmail.com Package for noise reduction in electron cryotomography with Anisotropic Nonlinear Diffusion. Support: Operating systems: Linux, Mac OS X Image format support: MRC Cost: Free for academic users Primary Publication to Cite: Fernandez, J.J. (2003). "An improved algorithm for anisotropic nonlinear diffusion for denoising cryotomograms". Journal of Structural Biology. 144: 152–161. doi:10.1016/j.jsb.2003.09.010. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help) Additional References: Fernandez, J.J. (2007). "Three-dimensional anisotropic noise reduction with automated parameter tuning. Application to electron cryotomography". Lecture Notes in Computer Science. 4788: 60–69. doi:10.1007/978-3-540-75271-4_7. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)

#### TOMOBFLOW

    Website: http://sites.google.com/site/3demimageprocessing/tomobflow Current version: 1.3 (July 2011) Contact: jjfernandez.software at gmail.com Package for noise reduction in electron tomography with Beltrami flow. Support: Operating systems: Linux, Mac OS X Image format support: MRC Cost: Free for academic users Primary Publication to Cite: Fernandez, J.J. (2009). "TOMOBFLOW: Feature-preserving noise filtering for electron tomography". BMC Bioinformatics. 10: 178. doi:10.1186/1471-2105-10-178. {{cite journal}}: Cite has empty unknown parameters: |pmcid= and |coauthors= (help)

#### XMSF

    Website: http://sites.google.com/site/xmsfilter/ Current version: 1.0 Contact: jbc747 at ual.es Package for noise reduction and pre-segmentation in electron tomography based on Mean-Shift. Support: Operating systems: Linux Image format support: Several, including SPIDER, MRC, IMAGIC, etc. Cost: Free for academic users Primary Publication to Cite: Bilbao-Castro, J.R. (2010). "XMSF: Structure-preserving noise reduction and pre-segmentation in microscope tomography". Bioinformatics. 26: 2786–2787. doi:10.1093/bioinformatics/btq496. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)

## Segmentation
#### CoDiv

    Website: http://coan.burnham.org Contact: coan@burnham.org CoDiv - Continental Divide Watershed Segmentation. Software for semi-automatic segmentation of density maps such as those obtained by electron microscopy and image reconstruction or electron tomography. Support: Operating systems: Linux Image format support: MRC Cost: Free for academic users Primary Publication to Cite: Volkmann N (2002). "A novel three-dimensional variant of the watershed transform for segmentation of electron density maps". J. Struct. Biol. 138: 123–129. PMID 12160708. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help)

#### Population

    Website: http://www.population-image.fr Current version: 2.0 Contact: ocds@shinoe.org CoDiv - Population is dedicated to the quantitative/qualitative analysis of images coming from 2D/3D microscopy with filtering, segmentation, geometrical/physical characterization, visualization and modeling. Support: Operating systems: Linux/Windows Image format support: RAW/BMP/JPEG/PNG/PGM Cost: Free for academic/industrial users, MIT Written In: C++ Primary Publication to Cite:

#### TOMOSEGMEM

    Website: http://sites.google.com/site/3demimageprocessing/tomosegmem Current version: 1.0 (December 2011) Contact: jjfernandez.software at gmail.com Package for segmentation of membranes in tomograms. Support: Operating systems: Linux, Mac OS X Image format support: MRC Cost: Free for academic users Primary Publication to Cite: Martinez-Sanchez A, Garcia I, Fernandez JJ (2011). "A differential structure approach to membrane segmentation in electron tomography". J. Struct. Biol. 175: 372–383. doi:10.1016/j.jsb.2011.05.010. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help)CS1 maint: multiple names: authors list (link)

#### TomoSegMemTV

    Website: http://sites.google.com/site/3demimageprocessing/tomosegmemtv Current version: 1.0 (April 2014) Contact: an.martinez.s.sw at gmail.com Package for robust membrane segmentation based on Tensor Voting for tomograms. Support: Operating systems: Linux, Mac OS X, Windows Image format support: MRC Cost: Free for academic users Primary Publication to Cite: Martinez-Sanchez A, Garcia I, Asano S, Lucic V, Fernandez JJ (2014). "Robust membrane detection based on tensor voting for electron tomography". J. Struct. Biol. 186: 49–61. doi:10.1016/j.jsb.2014.02.015. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help)CS1 maint: multiple names: authors list (link)

## B-Factor Estimation and Correction
#### bfactor

    Website: http://emlab.rose2.brandeis.edu/software Current version: 1.03 Contact: niko @brandeis.edu Program for filtering 3D maps and applying B-factors. Support: Operating systems: Linux/Mac Image format support: MRC Cost: Free/Open Source, GPL Primary Publication to Cite: Unpublished

#### EM-BFACTOR

    Website: http://sites.google.com/site/3demimageprocessing/embfactor Current version: 1.1 Contact: jjfernandez.software at gmail.com Package for sharpening high resolution information in single particle electron cryomicroscopy Support: Operating systems: Linux, Mac OS X Image format support: Most common formats used in 3DEM Cost: Free for academic users Primary Publication to Cite: Fernandez, J.J. (2008). "Sharpening high resolution information in single particle electron cryomicroscopy". Journal of Structural Biology. 164: 170–175. doi:10.1016/j.jsb.2008.05.010. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help) Additional References: Rosenthal, P.B. (2003). "Optimal Determination of Particle Orientation, Absolute Hand, and Contrast Loss in Single-particle Electron Cryomicroscopy". Journal of Molecular Biology. 333: 721–745. doi:10.1016/j.jmb.2003.07.013. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)

## Initial Model Construction
#### ROTAN

    Website: http://www.sickkids.ca/research/rubinstein/software/index.html Contact: john.rubinstein at utoronto.ca Program for estimating the relative angular orientation of single particles that present side views Support: Operating systems: Linux Image format support: MRC Cost: Free for academic users Primary Publication to Cite: Baker, L.A. (2008). "Angle determination for side views in single particle electron microscopy". Journal of Structural Biology. 162: 260–270. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help) Additional References: Rubinstein, J.L. (2003). "Structure of the mitochondrial ATP synthase by electron cryomicroscopy". EMBO Journal. 22: 6182–6192. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)