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Pipeline publication

[…] b'erialEM package (), for a total dose of \xe2\x88\xbc70\xe2\x80\x9380 electrons/\xc3\x852 per series. Images were recorded on a 2048\xc3\x972048-pixel CCD camera (Gatan, Pleasanton, CA, USA) at \xc3\x9738 500 magnification (7.8 \xc3\x85/pixel). Data were preprocessed and aligned using the IMOD software package (), with gold particles as fiducial markers., The final aligned tilt series were normalized and reconstructed using the simultaneous iterative reconstruction technique implemented in Tomo3D (). Individual virus particles were extracted from tomograms using IMOD. Tomograms were denoised by 100 iterations of anisotropic nonlinear diffusion (). The in-plane resolution of the full tomograms was in the 43\xe2\x80\x9355 \xc3\x85 range, as estimated using the Bsoft program TOMRES (). The extracted viruses were aligned to an icosahedral reference using maximum likelihood procedures for tomography as implemented in XMIPP (,)., Adenosome positions in each virus particle were defined by manual picking in the original, extracted 3D map (subtomogram) using IMOD. Only regions with gray levels higher than those of the background (outside the virus particle) were considered to represent adenosomes. Afterward, those positions were transformed according to the subtomogram alignment parameters so as to represent the adenosome positions in the aligned viruses. Panel (c) in Figure was created with UCSF Chimera\xc2\xa0)., The distributions of interparticle distances were calculated from a dataset consisting of pairwise distances for all pairs of adenosomes within each viral particle, then averaged across the 20 viral particle maps. The maximal inter-adenosome distance d is \xe2\x88\xbc70 nm, the internal diameter of the capsid. The number of adenosome pairs at large distances becomes progressively smaller, which simply reflects the finite size of the viral core. To obtain a quantity characteristic only of the interactions between the adenosomes and without the influence of finite size effects, we need to appropriately scale the distributions. The resulting scaled radial distribution function (RDF) shoul' […]

Pipeline specifications

Software tools Bsoft, Xmipp, IMOD, UCSF Chimera