usage: prog [options] This program will take a set of reference-free class-averages (or other projections) and generate a set of possible 3-D initial models. It does this by heavily downsampling the data, then running a number of very fast, full iterative refinements, each seeded with a random starting model. The results are sorted in order of apparent agreement with the data, such that at the end, the first numbered model should be the best result. Ideally the top few answers will all qualtitatively agree on the overall structure. If they do not, the results should be thoroughly assessed manually to insure a sensible result. By default this routine will generate 10 initial models, but this may be fewer or more than is strictly necessary depending on a number of factors. If the data is highly structurally heterogeneous, particularly if combined with a strongly preferred orientation, a correct solution using this technique may not be possible, but for most situations it will work well. For other situations, single particle tomography presents a good alternative for generating initial models.
| Option | Type | Description |
|---|---|---|
| --version | None | show program's version number and exit |
| --input | str | This file should contain good class-averages to use in constructing the initial model |
| --iter | int | The total number of refinement iterations to perform, typically 5-10 |
| --tries | int | The number of different initial models to generate in search of a good one |
| --shrink | int | Optionally shrink the input particles by an integer factor prior to reconstruction. Default=0, no shrinking |
| --sym | None | Specify symmetry - choices are: c<n>, d<n>, h<n>, tet, oct, icos |
| --automaskexpand | int | Number of voxels of post-threshold expansion in the mask, for use when peripheral features are truncated. (default=shrunk boxsize/20) |
| --randorient | None | Instead of seeding with a random volume, seeds by randomizing input orientations |
| --maskproc | str | Default=none. If specified, this mask will be performed after the built-in automask, eg - mask.soft to remove the core of a virus |
| --verbose, -v | int | verbose level [0-9], higher number means higher level of verboseness |
| --orientgen | str | The type of orientation generator. Default is eman:delta=9.0:inc_mirror=0:perturb=1. See e2help.py orientgens |
| --parallel, -P | str | Run in parallel, specify type:<option>=<value>:<option>=<value>. See http://blake.bcm.edu/emanwiki/EMAN2/Parallel |
| --ppid | int | Set the PID of the parent process, used for cross platform PPID |
For more information go to emanwiki/EMAN2/Programs/e2initialmodel.