commands of the programs used in the whole reconstruction process in cisTEM

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commands of the programs used in the whole reconstruction process in cisTEM

Dear All,

How can I get the commands that get executed for the processing. Say - Unblur is used for aligning the movies- what is the command used for that.



cistem program commands

Hi Andy,

Most programs are named as literally as possible. In your example, it is "unblur" (all lowercase) which will then give you a series of command line prompts for the options. This is of course assuming cistem is on your path. If you are using the precompiled binary, you can find the programs in the same directory as "cistem". You should have:


align_symmetry  calculate_fsc       ctffind                mag_distortion_correct  montage        refine3d               resize             unblur
applyctf        cisTEM              display                make_orth_views         prepare_stack  remove_inf_and_nan     scale_with_mask
apply_gain_ref  cisTEM_job_control  estimate_dataset_ssnr  make_size_map           project3d      remove_outlier_pixels  sharpen_map
apply_mask      console_test        extract_particles      merge2d                 reconstruct3d  resample               sum_all_mrc_files
calc_occ        convert_tif_to_mrc  find_particles         merge3d                 refine2d       reset_mrc_header       sum_all_tif_files


Each command line option has a default and a short message explaining what it does (at the prompt.)


These can be easily scripted.






cistem program commands with the options

Hi Ben,

Thanks. I do see all the programs in the cisTEM folder and on the terminal when the programs are invoked the options (input etc) do appear. What I am trying to get is there a way to see all the options and the usage of the program say 


type the program and hit return -- it provides the usage and the options

or anything similar, say

program -help



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