## Primary Bsoft papers

Heymann JB (2001) Bsoft: Image and molecular processing in electron microscopy. J. Struct. Biol. 133(2/3): 156 - 169.

Heymann JB and Belnap DM (2007) Bsoft: Image processing and molecular modeling for electron microscopy. J. Struct. Biol. 157(1): 3 - 18.

Heymann JB, Cardone G, Winkler DC and Steven AC (2008) Computational resources for cryo-electron tomography in Bsoft. J. Struct. Biol. 161(3): 232 – 242.

Heymann JB (2018) Guidelines for using bsoft for high resolution reconstruction and validation of biomolecular structures from electron micrographs. Protein Sci. 27(1):159-171.

## Radon package

Lanzavecchia S, Bellon PL and Radermacher M (1999) Fast and accurate three dimensional reconstruction from projections with random orientations via Radon transforms. J. Struct. Biol. 128: 152 - 164.

Lanzavecchia S, Cantele F, Radermacher M and Bellon PL (2002) Symmetry embedding in the reconstruction of macromolecular assemblies via the discrete Radon transform. J. Struct. Biol. 137: 259 - 272.

## Peach distributed processing system

Leong PA, Heymann JB and Jensen GJ (2005) Peach: A simple perl-based system for distributed computation and its application to Cryo-EM data processing. Structure 13(4): 505 - 511.

## Use of Bsoft

Dearborn AD, Wall JS, Cheng N, Heymann JB, Kajava AV, Varkey J, Langen R, Steven AC (2016) Alpha-synuclein amyloid fibrils with two entwined, asymmetrically associated protofibrils. J Biol Chem. 291(5): 2310 - 2318.

DiMattia MA, Watts NR, Cheng N, Huang R, Heymann JB, Grimes JM, Wingfield PT, Stuart DI, Steven AC (2016) The structure of hiv-1 rev filaments suggests a bilateral model for rev-rre assembly. Structure. 24(7): 1068 - 1080.

Fontana J, Cardone G, Heymann JB, Winkler DC and Steven AC (2012) Structural Changes in Influenza Virus at Low pH Characterized by Cryo-Electron Tomography. Journal of Virology, 86(6): 2919 - 2929.

Grünewald K, Desai P, Winkler DC, Heymann JB, Belnap DM, Baumeister W and Steven AC (2003). Three-dimensional structure of herpes simplex virus from cryo-electron tomography. Science 302(5649): 1396 - 1398.

Harris A, Cardone G, Winkler DC, Heymann JB, Brecher M, White JM, Steven AC (2006) Influenza virus pleiomorphy characterized by cryoelectron tomography. Proceedings of the National Academy of Sciences of the U. S. A. 103(50): 19123 - 19127.

Heymann JB (2015) Validation of 3d em reconstructions: The phantom in the noise. AIMS Biophys. 2(1): 21 - 35.

Heymann JB and Engel A (2000) Structural clues in the sequences of the aquaporins. J. Mol. Biol. 295: 1039 - 1053.

Heymann JB, Müller DJ, Landau EM, Rosenbusch JP, Pebay-Peyroula E, Büldt G and Engel A (1999). Charting the surfaces of the purple membrane. J. Struct. Biol. 128(3): 243 - 249.

Heymann JB, Pfeiffer M, Hildebrandt V, Kaback R, Fotiadis D, de Groot B, Engel A, Büldt G, Oesterhelt D. and Müller DJ (2000). Conformations of the rhodopsin third cytoplasmic loop grafted onto bacteriorhodopsin. Structure 8: 643 - 653.

Heymann JB, Cheng N, Newcomb WW, Trus BL, Brown JC and Steven, A.C. (2003) Dynamics of herpes simplex virus capsid maturation visualized by time-lapse cryo-electron microscopy. Nature Structural Biology 10(5): 334 - 341.

Heymann JB, Iwasaki K, Yim YI, Cheng N, Belnap DM, Greene LE, Eisenberg E and Steven AC (2005) Visualization of the binding of Hsc70 ATPase to clathrin baskets: Implications for an uncoating mechanism. Journal of Biological Chemistry 280(8): 7156 - 7161.

Heymann JB, Butan C, Winkler DC, Craven RC and Steven AC (2008) Irregular and semi-regular polyhedral models for Rous sarcoma virus cores. Computational and Mathematical Methods in Medicine, 9(3): 197 - 210.

Heymann JB, Winkler DC, Yim YI, Eisenberg E, Greene LE and Steven AC (2013) Clathrin-Coated Vesicles from Brain Have Small Payloads: A Cryo-Electron Tomographic Study. Journal of Structural Biology 184(1): 43-51.

Heymann JB, Bartho JD, Rybakova D, Venugopal HP, Winkler DC, Sen A, Hurst MRH and Mitra AK (2013) 3-dimensional structure of the toxin-delivery particle antifeeding prophage of Serratia entomophila. Journal of Biological Chemistry 288(35): 25276-25284.

Keller PW, Adamson CS, Heymann JB, Freed EO and Steven AC (2011) The HIV-1 Maturation Inhibitor Bevirimat Binds to and Stabilizes the Immature Gag Lattice. Journal of Virology, 85(4): 1420 - 1428.

Keller PW, Huang RK, England M, Waki K, Cheng N, Heymann JB, Craven R, Freed EO and Steven AC (2013) Retroviral CA can mature by a disassembly-reassembly pathway to produce viable virions or by a displacive pathway to produce aberrant virions. Journal of Virology 87(24): 13655-13664.

Nemecek D, Boura E, Wu W, Cheng N, Plevka P, Qiao J, Mindich L, Heymann JB, Hurley JH and Steven AC (2013) Novel fold and maturation pathway of a dsRNA virus capsid. Structure 21(8): 1374-1383.

Nemecek D, Heymann JB, Qiao J, Mindich L and Steven AC (2010) Cryo-electron tomography of bacteriophage φ6 procapsids shows random occupancy of the binding sites for RNA polymerase and packaging NTPase. Journal of Structural Biology, 171(3): 389 - 396.

Newcomb WW, Fontana J, Winkler DC, Cheng N, Heymann JB, Steven AC (2017) The primary enveloped virion of herpes simplex virus 1: Its role in nuclear egress. MBio. 8(3).

Ortega J, Heymann JB, Kajava AV, Rechsteiner M and Steven AC (2005) The Axial Channel of the 20S Proteasome Opens Upon Binding of the PA200 Activator. Journal of Molecular Biology 346: 1221 - 1227.

Pittet JJ, Henn C, Engel A and Heymann JB (1999) Visualizing 3D data obtained from microscopy on the Internet. J. Struct. Biol. 125: 123 - 132.

Schneider G, Guttmann P, Heim S, Rehbein S, Mueller F, Nagashima K, Heymann JB, Müller WG. and McNally JG (2010) Three-dimensional cellular ultrastructure resolved by X-ray microscopy. Nature Methods, 7(12): 985 - 987.

Sen A, Heymann JB, Cheng N, Qiao J, Mindich L and Steven AC (2008) Initial location of the RNA-dependent RNA polymerase in the bacteriophage φ6 procapsid determined by cryo-electron microscopy. Journal of Biological Chemistry 283(18): 12227 - 12231.

Trus BL, Heymann JB, Nealon K, Cheng N, Newcomb WW, Brown JC, Kedes DH. and Steven AC (2001). Capsid structure of Kaposi's sarcoma-associated herpesvirus, a gammaherpesvirus, compared to an alphaherpesvirus, herpes simplex virus type 1, and a betaherpesvirus, cytomegalovirus. J. Virol. 75(6): 2879 - 2890.

## Algorithms used in Bsoft

Belnap DM, Olson NH and Baker TS (1997) A Method for Establishing the Handedness of Biological Macromolecules. J. Struct. Biol. 120: 44 - 51.

Brinkmann G and Dress AWM (1997) A constructive enumeration of fullerenes. J. Algorithms 23, 345 – 358.

Cardone G, Grunewald K and Steven AC (2005) A resolution criterion for electron tomography based on cross-validation. J. Struct. Biol. 151(2): 117 - 129.

Cardone G, Heymann JB and Steven AC (2013) One number does not fit all: Mapping local variations in resolution in cryo-EM reconstructions. J Struct Biol. 184(2): 226 - 236.

Cowley JM (1995) Diffraction Physics. 3rd Rev. Ed. Elsevier Science, Amsterdam. (Multislice image simulation)

de la Fraga LG, Dopazo J and Carazo JM (1995) Confidence limits for resolution estimation in image averaging by random subsampling. Ultramicroscopy 60: 385 - 391.

Frangakis AS and Hegerl R (2001) Noise reduction in electron tomographic reconstructions using nonlinear anisotropic diffusion. J. Struct. Biol. 135(3): 239 - 250.

Frank J, Verschoor A and Boublik M (1981) Computer Averaging of Electron Micrographs of 40S Ribosomal Subunits. Science 214: 1353 - 1355.

Frey BJ and Dueck D (2007) Clustering by passing messages between data points. Science 315: 972 - 976.

Gobel U, Sander C, Schneider R and Valencia A (1994) Correlated mutations and residue contacts in proteins. Proteins 18: 309 - 317.

Hall SR (1991) The STAR file: A new format for electronic data transfer and archiving. J. Chem. Inform. Comput. Sci. 31: 326 -333.

Hall SR, Allen FH. and Brown ID (1991) The Crystallographic Information File (CIF): a new standard archive file for crystallography[1]. Acta Crystall. A47: 655 - 685.

Press WH, Teukolsky SA, Vetterling WT and Flannery BP (1992) Numerical Recipes in C. 2nd ed. Cambridge University Press, Cambridge. (Downhill simplex method of Nelder and Mead, Student's t-test, poisson distributed random numbers, LU decomposition, singular value decomposition, eigen analysis, factorial)

Saxton WO and Baumeister W (1982) The correlation averaging of a regularly arranged bacterial cell envelope protein. J. Microsc. 127: 127 - 138.

Unser M, Trus BL and Steven AC (1987) A new resolution criterion based on spectral signal-to-noise ratios. Ultramicr. 23: 39 - 52.

Winkelmann DA, Baker TS and Rayment I (1991) Three-dimensional structure of myosin subfragment-1 from electron microscopy of sectioned crystals. J. Cell Biology 114: 701 - 713.

## Software coopted in Bsoft

FFTW

Frigo M and Johnson SG (1997) The Fastest Fourier Transform in the West. MIT-LCS-TR-728 (September 1997)

Frigo M and Johnson SG (1998) FFTW: An adaptive software architecture for the FFT. In Proceedings of the ICASSP eds.), p. 1381.

Frigo M (1999) A fast fourier transform compiler. In Proceedings of the Conference on Programming Language Design and Implementation eds.), ACM SIGPLAN, Atlanta, Georgia.

FFTW 2.1.5 is distributed with Bsoft and is compiled as default. FFTW 3.x can be compiled externally and linked during compilation.

TIFF

Aldus (1992) TIFF revision 6.0. Aldus Corporation, Seattle, Washington.

PNG

JPEG

### XML

libxml2 is required for XML format parameter files.