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Bug #3422

closed

Fix magnification in Appion generated FREALIGN par file

Added by Melody Campbell about 9 years ago. Updated almost 9 years ago.

Status:
Closed
Priority:
Urgent
Category:
-
Target version:
Start date:
08/26/2015
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 2.2.0
Show in known bugs:
Workaround:

Description

The FREALIGN par file in appion i think is hardcoded to have a magnification of 10000. It should change based on the pixel size and the physical pixel size. To get the magnification, do: physical pixel size/pixel size * 10000.

So for Krios/K2 at scripps with a pixel size of 1.315, the mag is 5/1.315= 38022.

Physical pixel sizes for various detection devices:

K2: 5 µm
falcon ii: 14 µm
centra: 14 µm
Tietz: ? µm
US4000: 14 µm


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Related issues 2 (0 open2 closed)

Related to Leginon - Bug #3763: Camera physical pixel size for GatanK2 super-resolution mode is incorrectClosedAnchi Cheng11/12/2015

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Related to Appion - Bug #4088: uploaded images failed frealign preparation due to lack of sensor pixel sizeClosedAnchi Cheng04/06/2016

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