Just ignore those comments. They are hidden options. It should work anyway.
Sjors
On 02/05/2018 05:57 PM, Rui Yan wrote:
> Hi Sjors,
> I tried to add the arguments --use_all_data and --no_map to relion_refine, but they were reported as invalid Relion argument. I use the lastest Relion downloaded from Relion GitHub.
>
> My command line is:
> relion_refine --i Refine3D/job752/run_data.star --o Refine3D/job752/test/run2 --ref reference.mrc --ini_high 0 --dont_combine_weights_via_disc --pool 3 --ctf --ctf_corrected_ref --iter 0 --tau2_fudge 4 --particle_diameter 350 --K 1 --flatten_solvent --zero_mask --strict_highres_exp 10 --skip_align --sym C1 --norm --scale --j 8 --angpix 4.34 --no_map --use_all_data
> The following warnings were encountered upon command-line parsing:
> WARNING: Option --no_map is not a valid RELION argument
> WARNING: Option --use_all_data is not a valid RELION argument
> ......
--
Sjors Scheres
MRC Laboratory of Molecular Biology
Francis Crick Avenue, Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44 (0)1223 267061
http://www2.mrc-lmb.cam.ac.uk/groups/scheres
|