I want to do a local search/refine in cisTEM using the angles/shifts pre-determined by relion.
So I converted the star file from relion refine job into par file and import the par file into cisTEM.
But the angles/shifts are missing from cisTEM GUI.
Is there a way to recover the angles/shifts?
Are you importing the Relion Star directly, or you made a conversion yourself to par?
What angles and shifts are shown in cisTEM? Are you looking at results->3d refinement? You should see an angular plot and if you click on the document image above the angular plot it will show the imported angles.
I converted the star file from relion 3D refine job into a par file. I also merged the stacks from relion into one mrcs file. I checked the angles and shifts were in the par file.
Then I import the par file and mrcs file into cisTEM.
But in the Asset tab, the X pos and Y pos were all zero.
So is there a way to start a manual refine job in cisTEM based on parameters from relion?
Hi the X pos and Y pos in the asset tab are particle locations not shifts.
Have you tried looking in the results? Do you see a plot? Do you see parameters if you click on the pop out icon?
When I looked at the results->3D refinement, the FSC is a line all at 0, there is a plot for angular distribution, most of the plot is blue.
I did not find the "pop out icon" on this tab.
As I mention above it is the icon with an image of a document and a plus. It is located just above the angular plot.
This will tell you the exact angles assigned for each particle.
I found the angles and shifts are there indeed. But the occupancy, sigma and score are all zero. Should I change the occupancy and sigma to 1?
occupancy should 100, sigma i would put to 10, but 1 probably also fine.