Hi all,
I’d like to run Gctf on particle stacks with incoherent averaging of the power spectra, as described in the Gctf paper. I figure this might give better results than whole micrograph CTF estimation in cases where there are a lot of micrographs with polycrystalline gold or ice contamination in the frame. This works well on individual particle stacks, but when I attempt to do this on a whole dataset it complains that the stacks are of different sizes.
Is there an option to get around this? I thought --skip_check_mrc might do the trick but no luck. I can run gctf per stack in a for loop and then cat together the individual _extract.stars (for mic in mics/*mrcs; do Gctf-v1.06_sm_30_cu8.0_x86_64 $mic --mdef_ave_type 1 --resH 5 --do_Hres_ref --apix 1.07 --kV 300 --Cs 2.7 --ac 0.07 --do_EPA 1 --dstep 5.0 --do_validation --plot_res_ring --boxsize 512 ; done >& gctf_particle_stacks.log &) but just wondering if there is an option that I am missing.
Cheers
Oli
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