Converting Spider stacks

When converting stacks of 2D images from Spider to MRC you can use em2em. However, as jackmao explained, it is important to convert to a 3D volume somewhere on the way. Spider and IMAGIC both keep separate headers for each 2D image in a stack, but MRC format does not. You could use the SK command in Spider to convert your 2D images into slices of a 3D volume, and then convert this to MRC with em2em. Alternatively, you could convert your Spider stack first into an IMAGIC stack, then use the HEADERS command to convert the stack to a 3D volume (option WRITE - 3D_VOLUME), then use em2em to convert the 3D volume into MRC/CCP4.

A word about Spider format: If you would like to use Spider files with Frealign you can do so using the S option for the format in CARD1. However, a Spider stack always needs to be converted into a 3D volume where the x,y slices are the 2D images of your stack. Frealign does not currently read Spider stacks (where each 2D image keeps its own header).

Hi,

This is how I convert the spider stack to allow them readable by Frealign.
First, use SK command in SPIDER to convert your spider stack file, or a set of 2D files into a 3D volume spider file. In most cases, the 3D volume spider file, if each 2D slice in the volume has been normalized, it should be directly readable by Frealign. If not, then convert the 3D spider volume file into CCP4 volume file by em2em. The resulting CCP4 volume should be readable by Frealign. Note that the lastest MRC format is the same as CCP4 format. As Niko mentioned before, just use em2em to convert spider volume to CCP4 volume. Hope this is helpful to you.