cisTEM 1.0.0-beta: Auto refine error after iteration 1 finish

Hi,

I have imported star file and mrc stack from my Relion Extract folder and tried to run Auto Refine. It always finished the first iteration then returns with the errors below:

Error: File '/dev/null' couldn't be removed (error 13: Permission denied)

Error: Number of particles selected = 0; please change score threshold
From core/frealign_parameter_file.cpp:439
float FrealignParameterFile::ReturnThreshold(float, bool)

Please let me know if there were solutions. Thanks!

In the refinemnet package

In the refinemnet package that was created upon import - how many particles does it say it contains, and is this the expected number?

If you click display stack, does it show you the particles?

Thanks,

Tim

refinement package is okay

Thank Tim for your response,

The particle number match my expectation and they can be display properly.

In case the number makes a

In case the number makes a difference, there are 189361 ptcls

Can you go to the manual refine panel, and select local refinement for 1 iteration, and see if that works? If it doesn't, can you click on the expert options tab and change the "score threshold" to -10.0 and try again?

Thanks,

Tim

Manual refine finish 1 iteration

Hi Tim,

Manual refine 1 iteration and terminated normally, in fact if I ran for another 4,5 iterations they all terminated normally, although the result did not seem to be converging at all...

Hi,

If you create a new refinemnet package from your imported refinemnet package, but using the parameters from after the manual refine - I think the autorefine should work.

Thanks,

Tim

cisTEM 1.0.0-beta: Auto refine error after iteration 1 finish