makeboxref.py

Generates an optimal set of reference projections from a 3D model for use in automatic particle selection

makeboxref.py <threed file> [sym=<sym>] [ang=<dalt>] [phi=<dphi>] [nref=<# to gen>] [invert]

Parameters:


<threed file>Input 3D model
[sym=<sym>]Faster results if specified
[ang=<dalt>]Angular increment for initial projection generation. Generally the default is adequate
[phi=<dphi>]Angular increment for in-plane rotation. Generally default is adequate.
[nref=<# to gen>]Number of references to generate, ok to specify more than you need
[invert]Invert the contrast of the output projections (contrast must match micrograph being boxed)

Usage:

makeboxref.py threed.4a.mrc invert

Description

This program will generate a set of projections from a 3D model optimally sorted for use as references in particle autoboxing in 'boxer'. The output file (best.hed) contains an ordered list of projections sorted based on their mutual dissimilarity. That is, you may generate 50 or more references, but use only the first 10 or 20.

This file IS sorted, however, so you should ALWAYS use the first N particles in this file. The only decision to make is how large N should be. That is, how many references to use. Most particles will need at least 10 references for adequate boxing, and in many cases 30 or 40 is not unreasonable. To an extent this will depend on how much patience you have during the automatic selection process. See the 'boxer' manual for more information.


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