defocus values and image orientation

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Hi,

I'm not certain if this is a silly question but here goes. Is the convention for reading MRC files fixed, or does each program do its own thing? For example, is the first pixel (1,1) always at the same corner regardless of which program is reading the file? I'm asking this because I think ctftilt assigns the first pixel to be at the top left of the image, while EMAN's boxer program assigns it to be the lower left pixel. Having the wrong orientation will obviously be problematic when trying to CTF correct particles using values estimated with ctftilt but picked using boxer. I appreciate the help.

I believe that there is no

niko Mon, 2011-05-16 14:16

I believe that there is no agreed upon convention, unfortunately. In addition, different display programs will display an image differently. The only certainty I can offer is that pixel (1,1) is the first data value in the file and that the fast axis is the x-axis (i.e. the second data value is incrementing x). Therefore, to use the ctftilt information correctly, one has to do a careful comparison of conventions. On a more positive note, a future release of IMAGIC will have a function that will call ctffind3 or ctftilt and assign defocus values accordingly. This should make usage a bit easier.

Thanks Niko, that's what I

rkman Mon, 2011-05-16 14:48

Thanks Niko, that's what I was afraid of. I'll post it on the forum when I figure it out.

It should follow then that as

Axel Mon, 2011-05-16 15:29

It should follow then that as long as the order of the pixel values in the file is the same, then any differences in the display shouldn't matter so much, as long as all of the conventions after ctf correction are consistent with the ctffind3 conventions.

In other words, you should be able to pick your particles in boxer, box them out with batchboxer, then simply obtain the ctf with ctffind3. As long as the particles on the film are in the same orientation as after boxing (which they should be), then you won't have any problems.

If you are intending on using IMAGIC for later processing, there is an old post on how to convert ctffind3 output to the IMAGIC convention.

I hope this helps.