Question: I'm trying my first EMAN refinement, but the refine command crashes or produces black images in classes.1.hed. What's going on?
Answer: There are several possible causes for this. The first possibility is that your particles in start.hed and your initial 3D model in threed.0a.mrc aren't the same size. Do an 'iminfo start.hed' and 'iminfo threed.0a.mrc' and make sure they're the same size in pixels.
Aside from that, by far the most likely problem is that you used the 'ctfc=' or 'ctfcw=' options in the 'refine' command, but didn't properly prepare the input particles. With 'ctfit', 'fitctf' and/or 'applyctf'. The answer here is RTFM (read the _ manual). If you want to see if your particles are prepared for CTF correction run the 'eman' file browser, and look at the start.img file. In the text box below the image, you should see something like:
'!--2.38 252 1.22 0.15 0 6.84 2.54 1.43 400 4.1 2.7'
Your numbers will be different, of course, but there should be a row of numbers beginning with '!-'. If you don't see this, then your images haven't been properly phase flipped. .