usage: prog [options] [refine_xx] This program performs various assessments of e2refine_easy (or similar) runs, and operates in one of several possible modes. A refine_xx folder name must always be provided, except for resolution_all or resolution_vsref, which operate on all refine_xx folders: --timing will report how long each refinement took to complete as well as individual tasks within the refinement --timingbypath will report total timing information for each refine_xx folder, along with useful refinement parameters --resolution Computes per-iteration FSCs for a single refine_xx folder --resolution_all Computes FSC curves for the final iteration of every refine_xx folder --resolution_vsref Computes FSC curve for the final iteration of each refine_xx folder vs a provided reference volume. --evalptclqual This provides the ability to assess the agreement between individual particles used for a refinement and the final refinement itself in several critical ways. Using this option will automatically generate two new sets/ containing "good" and "bad" particles from the population used to run the specified refinement. The assessment is made using a set of heuristics. A multicolumn text file is also produced containing detailed results of the per-particle comparison (ptclfsc_XX.txt). The first line of this text file contains details about the meaning of each column: 0 - 100-30 it1 (integrated FSC from 100-30 A resolution for second to last iteration) 1 - 30-18 it1 2 - 18-10 it1 3 - 10-4 it1 4 - 100-30 it2 (integrated FSC from 100-30 A resolution for last iteration) 5 - 30-18 it2 6 - 18-10 it2 7 - 10-4 it2 8 - it12rmsd (RMSD between it1 and it2 integrated FSCs) 9-11 - alt1, az1, cls1 (orientation parameters for second to last iteration) 12-14 - alt2, az2, cls2 ( " for last iteration) 15 - defocus e2display.py --plot ptclfsc*txt (then adjust columns the plot displays, eg- 4 vs 5, 4 vs 6, 0 vs 4, 1 vs 5) --evalclassqual similar analysis to evalptclqual but for class-averages vs projections --anisotropy Assesses the amount and direction of any magnification anisotropy present in a raw data set by considering particles in a range of different orientations. Works best with large particles. Specify a class-average number for a class containing many particles (within a particular refine_xx folder). It is a good idea to compare results among classes in different highly occupied orientations. --extractorientptcl <output name> provides a way to extract particles with the alignment information for each particle stored in its header. Ostensibly such a data set could be run directly through e2make3d.py, but its primary use is with e2gmm.py and similar programs.
| Option | Type | Description |
|---|---|---|
| --version | None | show program's version number and exit |
| --timing | None | Report on the time required for each step of each refinement run |
| --timingbypath | None | Report on the CPU time required in each refine_xx folder |
| --resolution | None | generates a resolution and convergence plot for a single refinement run. |
| --resolution_all | None | generates resolution plot with the last iteration of all refine_xx directories |
| --resolution_vsref | str | Computes the FSC between the last iteration of each refine_xx directory and a specified reference map. Map must be aligned, but will be rescaled if necessary. |
| --evalptclqual | None | Evaluates the particle-map agreement using the refine_xx folder name. This may be used to identify bad particles. |
| --evalclassqual | None | Evaluates the class-average-projection agreement using the refine_xx folder name. |
| --extractorientptcl | str | Extracts the particles from a refinement with per-particle orientation information. If HDF output, will store as xform_align3d in header. |
| --anisotropy | int | Specify a class-number (more particles better). Will use that class to evaluate magnification anisotropy in the data. |
| --evalclassdetail | None | If specified with evalclassqual, will generate individual FRC curves for each class average in the even subset |
| --includeprojs | None | If specified with --evalptclqual, projections will be written to disk for easy comparison. |
| --iter | int | If a refine_XX folder is being used, this selects a particular refinement iteration. Otherwise the last complete iteration is used. |
| --mask | str | Mask to be used to focus --evalptclqual and other options. May be useful for separating heterogeneous data. |
| --sym | str | Symmetry to be used in searching adjacent unit cells, default from refine_xx parms |
| --threads | int | Number of threads to run in parallel on a single computer when multi-computer parallelism isn't useful |
| --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/e2evalrefine.