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Frequently asked questions

Juha Huiskonen edited this page Jul 20, 2016 · 19 revisions

###What is the format of the CMM file used to provide a vector defining a subunit of interest? The CMM file should have the following format. The first marker defines the start point of the vector (typically in the origin of the particle reconstruction) and the second marker defines the position of the subunit.

<marker_set name="marker set 1">
    <marker id="1" x="0.000" y="0.000" z="0.000" r="1" g="1" b="0" radius="10"/>
    <marker id="2" x="110.000" y="0.000" z="40.000" r="1" g="1" b="0" radius="10"/>
</marker_set>

###What does --align_subparticles option do? Option --align_subparticles will align the vector defining the orientation of the subunit on the Z-axis. For example, if the vector defines a 5-fold vertex of icosahedrally symmetric virus, this option will align the 5-fold axis of the reconstructed subparticle map on Z.

###Is there an easy way to define 5-fold (or 2-fold or 3-fold) axis of an icosahedrally symmetric particle? To create subparticles for subunits at icosahedral symmetry axis, use these vectors (this assumes the so called "I1 orientation"):

  • all 2-folds, use --vector 0.000,0.000,1.000
  • all 3-folds, use --vector 0.382,0.000,1.000
  • all 5-folds, use --vector 0.000,0.618,1.000
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