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refine particle xy shift different in Frealign and Xmipp #2382

Open leginonbot opened 5 months ago

leginonbot commented 5 months ago

Author Name: Anchi Cheng (@anchi2c) Original Redmine Issue: 2382, https://emg.nysbc.org/redmine/issues/2382 Original Date: 2013-06-05 Original Assignee: Dmitry Lyumkis

With MRC image stack and Xmipp Spider particle file data in the same orientation. The euler convention turns out to be the same once mirror in Xmipp is converted. However, the xy shift applied are different in the two packages. 3DEM convention did not include definition of the shift. Using EMX tentative convention (consistent with Xmipp), we will store in the database in that way.

This means the result of Frealign refinement need to be converted to what will be saved in the database. Reversed conversion is also needed when converted back.

leginonbot commented 5 months ago

Original Redmine Comment Author Name: Anchi Cheng (@anchi2c) Original Date: 2013-06-05T17:58:49Z

r17631 includes these changes. Note that this only works if the data orientation of Spider (used in Xmipp) and mrc (used in Frealign and Appion) 3D volume and image files are the same.

leginonbot commented 5 months ago

Original Redmine Comment Author Name: Dmitry Lyumkis (@LyumkisLab) Original Date: 2013-06-05T19:04:02Z

looks good to me ... unfortunately (for the headache that it causes), this sounds like the right thing to do ;)