Question: Is there anywhere that explains the text output of the classification and model construction routines? being impatient an dhaving calculated several completely bogus models of my asymmetric particle, I am hoping there is a way to tell fromt he numbers when it might be better to stop the procedure than to let it run on.
Answer: No, the docs don't really explain all of the text output at this point. I can tell you what the numbers are, but I don't think it's going to help you very much. While you may be able to judge the quality of an individual particle when compared to a good model using the quality factor, they really won't tell you what you're trying to find out. There are just too many variables involved.
If you're anxious that things are going too slow, the best approach is to increase the angular step for the first couple of refinement iterations. For an asymmetric model you could go as high as 15 or 18 degrees for the first round or two. That should be enough to tell you if the model is reasonable. You may also consider downsampling the data with, for example, proc2d start.hed newdir/start.hed shrink=2
As we tried to impress in the documentation, asymmetric models can be very tricky. It depends on their overall shape. If, for example you have something 'L' shaped, then getting a good starting model shouldn't be difficult at all. However, if you have something that's basically round with a few lumps, it may actually be impossible to generate an unabiguous accurate starting model. It is actually possible to have a set of random projections which can produce several DIFFERENT models, all of which are consistent with the data at some resolution.
StartAny uses c1startup, so no, there's no difference. The routine it uses isn't all that great. For 'easy' models it will work pretty well, but in tough cases, it may just come up with something completely wrong. In these cases, there are really only two good solutions in EMAN right now:
1) if your model may have a pseudosymmetry, ie - it's vaguely cylindrical in shape or something, you can often use the startcsym routine and get something that's good enough to start.
2) Final resort. Use tomography. If you're comfortable with it, then you might actually start here. Anyway, the idea is simple enough, take a tilt series (probably have to use stain or glucose for this). EMAN has a few experimental programs for generating a 3D model from the tilt series and aligning/averaging several such 3D models to generate a starting model. Even this approach isn't perfect (at least the simple implementation EMAN uses isn't), but we have used is with some success on a few projects.
To answer your question anyway: the output from classesbymra looks like:
0 -> 256 (506.86) 1 -> 296 (508.74) 2 -> 278 (502.86) 3 -> 273 (504.82)
The first line is saying that particle 0 (the first one in start.hed) looked the most like projection number 256. The quality factor was 506.86. The interpretation of the quality factors can depend on the shape of your model and the box size, etc.