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Bug #2382

open

refine particle xy shift different in Frealign and Xmipp

Added by Anchi Cheng over 11 years ago. Updated over 11 years ago.

Status:
In Code Review
Priority:
High
Category:
-
Target version:
-
Start date:
06/05/2013
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 3.0.0
Show in known bugs:
No
Workaround:

Description

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.

Actions #1

Updated by Anchi Cheng over 11 years ago

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.

Actions #2

Updated by Anchi Cheng over 11 years ago

  • Status changed from Assigned to In Code Review
  • Assignee changed from Anchi Cheng to Dmitry Lyumkis
Actions #3

Updated by Dmitry Lyumkis over 11 years ago

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

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