random value while adjusting the defocus in MF tool
Added by Anonymous almost 10 years ago
Hi,
when I use the measuring tool or click some where on the fft in MF gui i.e during live mode fft. The defocus step value changes automatically to some random value and when I click a +/- to change the defocus, it uses random value and if this value is operatable range it suddenly changes the defocus to a value like -900 micro-meter. It is not a big issue, if it is carefully adjusted. But for new users some times it is creating difficulties.
how to rectify this issue?
regards,
venkat
Replies (2)
RE: random value while adjusting the defocus in MF tool - Added by Anchi Cheng almost 10 years ago
Hi, Venkat,
Have you used this as a feature before ? If you left click on the power spectrum at where the first node is, Leginon calculates the defocus it represents and fill it in the settings as the increment for the +/- tool. That is how I adjust defocus now a day.
There are two known problems, though.
1. The algorithm is based on under focus values, but there is no easy way to tell that you are underfocus in the power spectrum. Therefore, you might guess wrong whether to add or subtract the defocus, nor would you know you over or under shot it when the correction is made. My workaround for the second problem is to always click slight outer of the node so that I always undershoot. Nothing can be done about the first problem.
2. I realized recently I hard coded the algorithm to use 200 kV HT. Will need to change that some time.
RE: random value while adjusting the defocus in MF tool - Added by Anonymous almost 10 years ago
Hi Anchi,
Thanks for the reply. Now it is more clear. Because I was always using the measure tool for the first zero, I think the first point I click at the center is filled in the settings as increment.
I was using the MF tool always, but never used to adjust the defocus using increment tool. Because the leginon computer is next to the microscope, I always try to check in DM by pausing the MF tool. But with Titan + K2 setup, if I pause the live mode and play it after checking manually in DM of K2 computer, most of the times the connection to the DM computer (host) is lost and I have to restart the leginon and leginon clients in both the computer to re-establish the connection.
best,
venkat