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| The answer depends on the source images. EMAN reads most EM file formats directly. If you have each particle in a separate image file, for example, img001.img, img002.img, etc., then the following command would do it (zsh, similar for other shells): | '''Question:''' If I have particles already picked and 'extracted' using a picking software other than 'boxer', how can I put them all into a '.hed' file so as to use them with EMAN? |
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| foreach i (img*.img) proc2d $i start.hed end |
''' ''' '''Answer:''' The answer depends on the source images. EMAN reads most EM file formats directly. If you have each particle in a separate image file, for example, img001.img, img002.img, etc., then the following command would do it (zsh, similar for other shells): foreach i (img*.img) proc2d $i start.hed end |
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| for i in img*.img proc2d $i start.hed |
for i in img*.img proc2d $i start.hed |
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| All of the 2D EMAN commands currently write Imagic files by default. 3D commands write MRC format by default. There are options in proc2d and proc3d for writing to other file formats. | All of the 2D EMAN commands currently write Imagic files by default. 3D commands write MRC format by default. There are options in proc2d and proc3d for writing to other file formats. |
Question: If I have particles already picked and 'extracted' using a picking software other than 'boxer', how can I put them all into a '.hed' file so as to use them with EMAN?
Answer: The answer depends on the source images. EMAN reads most EM file formats directly. If you have each particle in a separate image file, for example, img001.img, img002.img, etc., then the following command would do it (zsh, similar for other shells):
foreach i (img*.img) proc2d $i start.hed end
-or- (csh)
for i in img*.img proc2d $i start.hed
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 2D EMAN commands currently write Imagic files by default. 3D commands write MRC format by default. There are options in proc2d and proc3d for writing to other file formats.