
| <particles> | Raw particle filespec |
| <refrences> | Reference image filespec |
| <number of sets> | Number of different reference sets |
| [frac=<num>/<denom>] | Operate only on a fraction of the raw images |
| [verbose[=<n>]] | More verbose output |
| [mask=<rad>] | Mask the classified particles, also reduces noise for better classification |
| [imask=<rad>] | Inside mask, classified particles are masked for classification, but not in the cls files. |
| [precen] | Particles are assumed to be accurately precentered |
| [sigfilt] | Apply a real space filter so only high amplitude data is used for classification |
| [ctfc] | Projections are CTF corrected |
| [shrink=<n>] | Shrink the particles before classification by speed |
| [refine] | Refines 2D alignment done with fast algorithm. Slower, but not 'slow'. |
| [slow] | Uses a very slow, exhaustive search algorithm for alignment |
| [phase] | Experimental. Uses pcmp(), a weighted mean phase-error to compare images for classification |
| [wtphase] | Experimental. Uses pcmp with a SNR weight. |
| [fscmp] | Experimental. Uses fscmp(), a weighted mean phase-error to compare images for classification |
| [wtfscmp] | Experimental. Uses fscmp with a SNR weight. |
| [usefilt] | Experimental. Use the 'filt' version of the input file for classification. |
classesbymra2 start.hed proj.hed 2 mask=28 ctfc
This classifies a set of raw particles based on multiple sets of reference projections. The output is a set of cls*.img files, one file for each reference image. If the projections were generated from a CTF corrected model, specify the 'ctfc' option so the projections will be 'decorrected' before classification.
This is basically a modified version of classesbymra. In this case, a set of numbered
directories must exist in the current directory, ie - '1', '2', '3', etc. The file
EMAN Manual page, generated Tue May 25 14:15:51 2004