usage: prog [options] [classes file] This program will go through a standard classes file (containing EMAN2-generated class-averages), and extract the particles associated with one or more class-averages. Some similar tasks can be performed graphically with e2evalparticles.py. This program is used by e2refinemulti to extract particles associated with each of the output volumes for subsequent single-model refinement. There are 3 mutually exclusive modes in this program: --refinemulti - Extracts the particles associated with each of the output 3-D maps generated by an e2refinemulti run --classlist - Extracts references to all of the particles in a user specified list of class numbers (the list of integers is in a text file) --orientedparticles - Extracts rotated/translated particles associated with each class-average into a separate stack (also requires --orientcls) Examples: Extract all of the 2-D aligned even and odd particles associated with a specific class-average: e2classextract.py --orientcls refine_03/cls_result_04 --orientedparticles sets/all_ctf_flip_fullres --evenoddmerge --orientclassn 248
| Option | Type | Description |
|---|---|---|
| --version | None | show program's version number and exit |
| --refinemulti | None | Extracts particles based on the model_id header value in each class-average, normally produced by e2refinemulti |
| --classlist | str | Filename of a text file containing a (comma or whitespace separated) list of class average numbers to operate on. |
| --orientedparticles | str | Filename of the set (.lst file) with the particles used for the --orientcls file |
| --orientcls | str | Filename of a cls_result_xx or classmx_xx file. |
| --orientclassn | str | Specify a comma separated list of class numbers to extract in oriented particles mode. |
| --input_set | str | Normally the set used to create the class-averages is used as input. Use this with another version of the same set of particles, for example '__ctf_flip_proc' instead of '__ctf_flip' |
| --setname | str | Name of the stack to build |
| --evenoddmerge | None | with --orientedparticles, if cls_result_xx is specified, will include both _even and _odd particles in the output. |
| --excludebad | None | Excludes the particles from the generated set(s). They are included by default. |
| --noderef | None | If particle file was .lst, normally the output .lst will reference the original image file. With this option, the output will reference the .lst file instead, creating a lst pointing to another lst. |
| --sort | None | If set, output .lst file will be sorted. The default is to leave the output grouped by class-average. If (and only if) sorted, duplicate entries will be removed. |
| --ppid | int | Set the PID of the parent process, used for cross platform PPID |
| --verbose, -v | int | verbose level [0-9], higher number means higher level of verboseness |
For more information go to emanwiki/EMAN2/Programs/e2classextract.