Leginon

Hi,

I am collecting a tilted dataset and want to use Gctf to do per-particle CTF estimation. In the Appion page for Gctf, there is a section labeled "Tilt Refinement Parameters". Does this flag do per-particle CTF estimation, or just estimate a tilt across the entire micrograph?

Additionally, I tried to use the tilt refinement flag and got an error saying that flag does not exist.

Here is the command that was generated in Appion and the error that I got when I tried to run it. Is this a simple issue of version incompatibility, etc.?

Thanks for any help!
Rick

gctf.py --ampcontrast=0.1 --defstep=0.1 --dast=0.1 --resmin=50 --resmax=4 --fieldsize=1024 --do_EPA --mdef_aveN=7 --refine_tilt=0 --init_tilt_ang=20 
--max_phase_shift=180 --min_phase_shift=0 --phase_search_step=1 --phaseplate --runname=gctfrun1 --rundir=/data/microscopes/appion/17may30a/ctf/gctfrun1 
--preset=en-a --commit --projectid=20 --session=17may30a --no-rejects --no-wait --continue --bestdb --fastmode --expid=886 --jobtype=gctf

 ... Time stamp: 17may31p09
 ... Function name: gctf
 ... Appion directory: /data/software/repo/myami/3.3-alpha/lib/python2.7/site-packages
 ... Processing hostname: giovanni.al.ucsd.edu
Usage: gctf.py --projectid=## --runname=<runname> --session=<session> --preset=<preset> --description='<text>' --commit [options]

gctf.py: error: no such option: --refine_tilt