Dear Sjors,
I have recently started using Relion-1.3 but am having some problems with the autopicking function. To test the function I followed instructions on the Relion-wiki pages:
1) I ran CTFFIND3 on several raw micrographs (mrc format) without any issues
2) Created a new STAR file containing the two micrographs with highest and lowest defocus values from the relion_display program. This file was used as my INPUT for the autopicking
3) My reference file was the data.star file output from a 2D-classification run from Relion1.3. This 2D-classification was run on particles picked and CTF corrected outside of Relion but otherwise preprocessed in Relion-1.2
4) Run relion_autopick in sequential mode with "Write FOM maps? - Yes"
However, when I run relion_autopick from the GUI it does not generate FOM maps (no .spi files) or coordinate STAR files. Below is the terminal output.
Executing: `which relion_autopick` --i NorR_Q304E_140618_Test.star --o autopick --particle_diameter 240 --angpix 2.05 --ref run3_it025_data.star --invert --ctf --ang 5 --lowpass 20 --write_fom_maps --threshold 0.25 --min_distance 40 &
Run autopicking on the following micrographs:
* NorR_Q304E_140618_0034.mrc
* NorR_Q304E_140618_0036.mrc
When I open a micrograph and tick pick particles, ensuring the rootname is the same, there are no picked particles.
Therefore, I have several questions:
1) Is there a problem that the original micrographs were mrc format?
2) You mention that you can convert micrographs to STAR using relion_star_all_micrographs but this program isn't available in the Relion-1.3 directory we have downloaded, have I missed something in how to use this function?
3) Could the problem be that my 2D classification reference file was created in relion-1.2 or that the particles for this reference file were CTF corrected outside of Relion
4) Have I chosen the correct reference file? - data.star
5) Or am I doing something wrong in the Relion-1.3 GUI?
Thankyou very much in advance,
Kind regards,
Dominic Pollard
PhD student Imperial College London
Center for Structural Biology
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