Appion

How about this one:

12dec22a_gr2_00012gr_00013sq_v01_00033hl_00004ed.mrc

logfile: /ami/data00/appion/12dec22a/ddstack/ddstack2/12dec22a_gr2_00012gr_00013sq_v01_00033hl_00004ed_st_Log.txt

or this one:

12dec22a_gr2_00012gr_00013sq_v01_00009hl_00003ed.mrc

logfile: /ami/data00/appion/12dec22a/ddstack/ddstack2/12dec22a_gr2_00012gr_00013sq_v01_00009hl_00003ed_st_Log.txt

and here's one that appears highly drifty / astigmatic, and I can't seem to be able to correct it (the scope was coma-free aligned)

12dec22a_gr2_00012gr_00013sq_v01_00012hl_00002ed.mrc

logfile: /ami/data00/appion/12dec22a/ddstack/ddstack2/12dec22a_gr2_00012gr_00013sq_v01_00012hl_00002ed_st_Log.txt

...

I have been going through the directory "ddstack2" to try and pick out good examples. A number of the images do seem to align. The way I am judging this is by looking at the shifts, and in select cases at the FFTs. For about 1/2 of the images, The shifts follow a specific trend, which is expected for a 5-second exposure (e.g. from -4 to 4 pixels). For the other half, there is no trend and the shifts fluctuate randomly around +/-1 (you can test this, for example in bash, `for file in *ed_st_Log.txt ; do tail -22 $file ; done`). The FFTs for these images don't look terrible, but the signal is weak, weaker than in my previous data. In addition, many of them appear astigmatic, even though I know the scope was well aligned, which you can see from the coma-free tableuas in the data. Perhaps this is all due to a weak signal, since the thon rings are consistently weaker than in my other session, 12dec05a.

For example, compare any image from 12dec22a with this image from 12dec05a, which doesn't even have any carbon in it:

12dec05a_gr1_00012gr_00057sq_v01_00006hl_00003ed-a.mrc

or, more comparable images (and FFTs)

12dec05a_gr1_00012gr_00057sq_v01_00007hl_00003ed-a.mrc ...... vs. ...... 12dec22a_gr2_00011gr_00031sq_v02_00021hl_00003ed-a.mrc

feature #2216 allows the specification with the image id of the required image.

I tested on 12dec22a_gr2_00012gr_00013sq_v01_00033hl_00004ed.mrc and the alignment result (on defcon1) is not jumping.

I still need to find out why it failed previously, but this will keep you moving.

Yes, this is much better than the previous logfile. Did you do anything different, apart from specifying the reference image? (I don't remember if I was trying to run on amibox04 or defcon1). What is the reference image (2026767)? Which table are they located in, and what reference images should I be trying?