Changing pixel size
Added by Rick Baker about 6 years ago
Hi,
when we first installed our Talos Arctica we calibrated the exposure mag pixel size in micro-probe mode. We have recently switched to only using nano-probe mode, but our pixel size has changed from 0.6 to 0.58 ang/pixel.
This is a problem for CTF estimation in Appion, as it still assumes the 0.6 ang pixel size. As an example, the same micrograph has an estimated defocus of 0.9517 um (est good fit to 3.2 Ang) with the 0.58 pixel size and 1.0148 um (est good fit to 3.5 Ang) with the 0.6 pixel size.
How can we change the pixel size so that Appion is using the correct value? Is it the value stored in Leginon for the exposure preset? Or is it a value somewhere in the Appion database?
Finding this in the wiki is kind of hard considering how many results come up when you search "pixel size" :)
Thanks!
Rick
Replies (1)
RE: Changing pixel size - Added by Anchi Cheng about 6 years ago
Yes, redmine search is pretty bad in keeping the more important results on top.
For future images, you can change pixel size through Calibration Application PixelSize node.
Send the preset of the correct scope/camera pair in PresetsManger to initialize it.
And then follow what you should do for known pixel size.
http://emg.nysbc.org/projects/leginon/wiki/Pixel_Size_Calibration
The database does retain the pixelsize of the old images, though. If you need to change those, you will have to modify it directly but may sure you retain the DEF_timestamp.