The answer depends on the source images. EMAN currently knows how to read MRC, IMAGIC, Spider and PGM/GIF/TIFF (with some restrictions). If you have each particle in a separate image file, for example, img001.img, img002.img, etc., then the following command would do it:
foreach i (img*.img) proc2d $i start.hed end
It doesn't matter what file format the source images are in. Any EMAN program transparently reads any supported image type (byte order doesn't matter either). If the images are already in a Spider stack file called, for example, part.spi, the following would do it:
proc2d part.spi part.hed
All of the EMAN commands currently write Imagic files by default. There are
options in proc2d for writing to other file formats.
Your first attempt might be to use symbest, or perhaps footprint
combined with classesbymra. These techniques might work well if you have
particularly strong data (ie - negative stain or high dose ice images). If you
have typical ice images, you'll probably have to try to do simultaneous refinements
with the refine2 command. This command allows you to simultaneously
refine several different 3d models from a single set of particles. By using
starting models representative of each possible symmetry, the refinement
should reveal which model best represents the data. Unfortunately this command is
still considered experimental in this release. It should work fairly well, but
it does not yet have the full set of options available to the refine
command.
There are 2 causes for this. The 'help' option uses netscape to provide the requested information. For this to work, netscape must be running on your local x-windows display. The other possible problem is when you are running EMAN on a remote computer. By default, the 'help' option displays manual pages from the local copy of the manual you installed with EMAN. If netscape is running on the local computer, and EMAN is running on the remote computer, netscape can't find the help files you're asking for. The solution for this is to do the following:
cd ~ echo >.eman/remotehelp
After doing this, the 'help' option will display manual pages directly from the NCMI server. The only potential problem with this is that you might be looking at manual pages that are newer than the version of EMAN running on your local machine.
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