Bug #4835
openHow does Appion supply the defocus value to CTF estimation programs?
0%
Description
User on the microscope has a preset set at -2 um for nominal defocus, but that is not the value that is provided to CTFFind4. Given that they are doing a tilt data collection, does Appion try to compensate?
For example:
Filename: 17mar15a_grid1_00028gr_00001sq_v02_00002hln_v01_00002enn-a.mrc
Size: 54.32 MB
Acquired: 2017-15-03 10:07:18
Path: /gpfs/leginon/ygomez/17mar15a/rawdata/
Session: 17mar15a - polZ no det, tilt 30-40
Instrument: Krios - GatanK2Counting
Scope Host: titan52334860
en preset:
mag: 22500 defocus: -2.00 μm pixelsize: 1.10 Å dose: 74.48 e–/Å2 tilt: -30.0°
en-a preset - CTFFind4 estimation:
runname: ctffind4run2 nomDef: -2.98 μm def1: 3.06 μm def2: 3.11 μm θastig: -60.78 amp con: 7.00E-2 cs: 2.70
res (0.8): 7.28 res (0.5): 7.07 conf (appion): 0.98 res (pkg): 6.93 Å conf (pkg): 0.98
In the Image Data tree:
Data > scope > defocus = -2.98 um
Data > scope > focus = -0.00254749943596904
Data > preset > defocus = -2.00 um
Updated by Anchi Cheng about 7 years ago
- Project changed from 138 to Appion
- Status changed from New to Assigned
- Assignee set to Anchi Cheng
- Affected Version set to Appion/Leginon 2.2.0
The example image is from a tilted image with image shift targeting. When it is this situation, Leginon need to compensate for difference in specimen height when it is away from the tilt axis. Therefore, the value that actually sent to the scope is different from the preset value. I will change the way the value is retrieved from the database so that it represent that of the preset, not the scope value.
Updated by Anchi Cheng over 5 years ago
- Related to Bug #6538: defocus offset correction for beam-image shift are used in myamiweb and Appion as intended defocus. added