When I run e2ctf_auto.py from e2projectmanager.py with --lores option, the pre-processed particle stacks are created correctly:
$ ls particles/
mic-name.hdf
mic-name__ctf_flip_lp12.hdf
mic-name__ctf_flip_lp20.hdf
mic-name__ctf_flip_invar.hdf
...
However, when the subcommand e2buildsets.py --setname=all --excludebad --allparticles --withflipped is run by e2ctf_auto.py, the following error is raised:
ERROR: No images left to include after applying filters!
And thus the folder sets is empty. I checked the code and in --lores mode e2ctf_auto.py does not create the __fullres.hdf files. These files are checked by e2buildsets.py when option --withflipped is used (see lines 122-125). In all other modes (hires, midres) e2ctf_auto.py does create __fullres.hdf. So there are two possible solutions:
A) add a subcommand to produce __fullres.hdf in all cases inside e2ctf_auto.py
B) change the way how --withflipped works. Perhaps, it could check if __lp??.hdf files exist...
Many thanks!
Vadim
PS Yes, we still do negative stain single-particle in 2022 ;)
Dear EMAN2 team,
When I run
e2ctf_auto.pyfrome2projectmanager.pywith--loresoption, the pre-processed particle stacks are created correctly:However, when the subcommand
e2buildsets.py --setname=all --excludebad --allparticles --withflippedis run bye2ctf_auto.py, the following error is raised:And thus the folder
setsis empty. I checked the code and in--loresmodee2ctf_auto.pydoes not create the__fullres.hdffiles. These files are checked bye2buildsets.pywhen option--withflippedis used (see lines 122-125). In all other modes (hires, midres)e2ctf_auto.pydoes create__fullres.hdf. So there are two possible solutions:A) add a subcommand to produce
__fullres.hdfin all cases insidee2ctf_auto.pyB) change the way how--withflippedworks. Perhaps, it could check if__lp??.hdffiles exist...Many thanks! Vadim
PS Yes, we still do negative stain single-particle in 2022 ;)