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Adrian Quintana edited this page Dec 11, 2017 · 1 revision

angular_distribution_show

Purpose

This program shows which is the angular distribution of a set of projections. There are four kinds of outputs: a bild file (chimera understands this format), an OpenDX file, a distance histogram and a topological sphere. The OpenDX file can be used as input of the network /ang_distribution.net to visualize the angular distribution with OpenDX. The topological sphere is shown with small isosceles triangles (the longest part is pointing to Y in the projection plane) and the distance histogram is the distance (only measured on the sphere surface) between projections. This is an objective measure of the distance between projections. (Note, if the -DX flag is used arrows are used instead of triangles)

Usage


$ angular_distribution_show ...

Parameters

  • `` A metadata file with the angles. If there is a weight column, then triangles are generated with variable size. This size depends linearly on the value in the corresponding column of the document file. The value given for-r will be the largest triangle

For_openDX_ output:

  • `` Output file used as input for the openDX net. The network supplied (see bellow) assumes that the DX file name isout

For_chimera_ output:

  • `` Output file used as input for chimera.
  • `` only works for -bild and allow to shift the system of coordinates center.

For_Distance Histogram_ output:

  • `` Output file for the histogram of projection distances
  • -steps [stepno100] = Number of steps in the histogram
  • `` Show distances and vector positions while being computed

For the_Topological Sphere_ output

  • `` Output file for the topological sphere
  • -R [Radius60] = Radius of the topological sphere
  • -r [side1.5] = Triangle side
  • -rot_view [rot0] = Point of view in the topological sphere
  • -tilt_view [tilt30] = Point of view in the topological sphere,tilt_view0= are top views, andtilt_view90= are side views
  • `` If there are projections in the bottom topological semisphere and this option is set, then they are reflected to the upper semisphere
  • `` The projection sphere is made solid (instead of transparent). In this way, projections in the rear part of the sphere are not shown

Examples and notes

Topological sphere:


$ angular_distribution_show -sel uneven_distributed.sel -ps ang_distrib.ps -tilt_view 60

The result is:

/uneven_60.gif

The distance histogram for this distribution is:

/uneven_60_hist.gif

is obtained with



$ angular_distribution_show -sel uneven_distributed.sel -hist ang_distrib.hist -steps 25

generate out forOpenDX


angular_distribution_show -sel img.sel -DX img

generate out for chimera


angular_distribution_show -ang refangles.spi -bild test.bild  -R 100 -order  psi tilt rot -wcol 3 -r 7.5 -shift_center 70

Note: refangles.spi contains four columns three with angles and the fourth one with the number of particles

Note: -shift_center should be half the volume size, and -R should be 2/3 the volume size

/jaime.jpg

User Comments

--Main.AlfredoSolano - 29 Jan 2007

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