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**Question:** How can I find out how many particles were used in a reconstruction ? How can I look at the particles that were discarded ?

**Answer:** Good questions! To find out how many particles were included in the class-averages, type (for example) 'iminfo classes.4.hed all'. The last number on each line is the number of particles included in that class-average. At the end a total number of particles included in the classes file will be shown.

Now this is where it gets tricky. If all of the class-averages were used in the reconstruction, you'd be done. However, some class-averages may get excluded (depending on the value you select for hard=). However, they are not necessarily the same class averages that are excluded from the original make3d reconstruction. make3d will output how many original particles were included in the final reconstruction as part of its output on the screen. This is probably the best answer you'll get, but it isn't stored anywhere. Generally when I talk about the number of particles used in a reconstruction, I'm referring to the 'iminfo classes.4.hed all' method. 

**Note:** In current, post 1.8 snapshots, the  particle.log file now stores how many particles were used in make3d.

The next part is a little trickier. A complete record of particles excluded from the class-averages is kept (along with classification information) for all iterations, in 'particle.log'. This file has a variety of different information in it, depending on the first character of the line. Lines starting with 'X' indicated excluded particle numbers. If going through this file is too much of a pain, you can rerun the 'classalignall' command with the 'badfile'. This will create a set of files containing the excluded images for whatever options you provide to classesbymra.

Note that the particle.log file can also be used to recreate the 'cls' files from any particular iteration using the 'clsregen' command.