Dear developers:
I have met the same issue as described in https://cistem.org/cistem-100-beta-auto-refine-error-after-iteration-1-finish.
I import the STAR file and mrc stack from Relion extraction (with refined angular information included). First, the manual refinement works fine. Then, the auto refinement works fine , too.
However, when I run ab initial model generation and use the resulting model as the reference of auto refinement, the error occurs at the second iteration:
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)
Any suggestions? Thanks in advance!!
Hi,
Can you try running 1 round of local refinment at 20A in the manual refine panel. Then go to the refinement results panel, and export the parameters from that refinement as a .par file. Then import a new refinement package, selecting the same stack, but using the frealign parameter file you just exported. Double check the contrast of the particles in the stack and make sure you select the correct entry upon import.
I believe this should work for the auto-refine.
Thanks!
Tim
Yes, it works, thanks for the help!