project3d

Generate projections of a 3D model

project3d <input file> [out=<file>] [prop=<dtheta>] [perturb] [4point[=<az>]] [euler=<alt>,<az>,<phi>] [list=<euler file>] [spiral=<angles>] [grid=<steps>] [reproj=<class file>] [mask=<radius>] [text] [sym=<c4,icos,etc>] [icos5fhalfmap] [pad=<newsize>] [mode=<1-6>] [phitoo[=<ang>]] [smear] [phicomp] [randomphi] [randomall[=<altmin>,<altmax>,<azmin>,<azmax>,<phimin>,<phimax>]] [frac=<0 to d-1>/<d>] [minalt=<ang>] [makemask] [mrc2voltable]

Parameters:


<input file>3D model to be projected
[out=<file>]Output file. Default is 'proj.img'
[prop=<dtheta>]Most common option. Generates projections with a relatively uniform projection density in the unit triangle.
[perturb]Used with prop to generate variations within the Euler angle distribution to reduce deterministic artifacts in Fourier space
[4point[=<az>]]Generates 4 projections. 1 polar and 3 equatorial. Optional Az will rotate the top view.
[euler=<alt>,<az>,<phi>]Generate a single projection with the given orientation
[list=<euler file>]Generate projections from a list of orientations
[spiral=<angles>]Generate projections along a spiral from axis to equator
[grid=<steps>]Generate projections on an rectangular alt/az mesh, nonuniform projection density
[reproj=<class file>]Give the name of a file with class-averages, and the model will be reprojected at corresponding angles.
[mask=<radius>]Specify a circular mask radius for the projections
[text]Dumps Euler angles to a text file
[sym=<c4,icos,etc>]Specify symmetry of model to prevent redundant projections
[icos5fhalfmap]Specify that the input map is an icos 5f map
[pad=<newsize>]Used in Fourier mode
[mode=<1-6>]Default is real-space projection, this specifies various Fourier modes
[phitoo[=<ang>]]This will also vary phi in the final file. Warning: This works only with prop= and generates a LOT of projections.
[smear]Used in conjunction with 'phitoo', this will rotationally smear between phi steps.
[phicomp]This will roughly compensate for in-plane rotation from az with phi
[randomphi]Randmomize phi (usually zero in most modes)
[randomall[=<altmin>,<altmax>,<azmin>,<azmax>,<phimin>,<phimax>]]Randomize all 3 Eulers.
[frac=<0 to d-1>/<d>]Generate a subset of the projections, used for parallel processing
[minalt=<ang>]Minimum projection altitude
[makemask]This will generate a output mask rather than a projection
[mrc2voltable]For large maps, this option can save memory by reading directly into a masked memory structure

Usage:

project3d threeed.4a.mrc prop=5 sym=c4

Description

This program generates a set of projections from a 3D model. Fourier space projection is much faster than real-space projection, but also produces fairly severe artifacts (much more severe than Fourier space reconstruction). This effect can be viewed with v4 The default 'mode' is -1, which is real-space projection with trilinear interpolation. This produces artifacts in Fourier space, but is quite good in real space. If mode > 0, the mode specifies the interpolation size in voxels. That is, mode=3 denotes 3x3x3 Gaussian interpolation in Fourier space. For most purposes, the default mode of -1 should be used.

The orientations to use for projections can be specified many different ways. The spiral option produces the most uniform projection density in the unit triangle, but has a pitch, since it is a spiral. This pitch can produce artifacts in a refinement. The prop option generates nearly as uniform a distribution as spiral, but without this artifact.

For prop=, the ang parameter is the angular spacing between altitudes in degrees. The azimuthal spacing is proportional to sin(alt).

Minalt is used for helical reconstructions to produce near side-views only. For example, minalt=80 will produce projections ranging from side views to a 10 degree tilt.


EMAN Manual page, generated Wed Feb 18 10:33:43 2009