local refine from relion priors

Dear all,

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?

Thanks,

Lei

Hi Lei,

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.

Thanks,

Tim

Import from par file

Hi Tim,

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

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?

Tim

When I looked at the results-

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

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.

Tim

I found the angles and shifts

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

occupancy should 100, sigma i would put to 10, but 1 probably also fine.

Tim