$def with (form, dirs) Clip, Motioncor2, Gctf parameters form

This form helps you configure the motioncor2 automatic runs for one directory.

$if not form.valid:

Try again, invalid input:

$:form.render()
Will run on each TIFF: 
    
clip unpack -D "Defects filename"
            -R 1 (if checkbox "Rotate gain" is activated)
            "Gain filename"
    
MotionCor2 -FtBin   "Binning"
           -FmDose  "Dose per frame"
           -PixSize "Pixel size"
           -Throw   "Initial frames to ignore"
           -Group   "Group frames before aligning"
           -kV 300 -Patch 5 5 -RotGain 3
           
gctf --kV 300
     --Cs 0.01
     --ac 0.1
     --dstep 5.0
     --do_EPA 1
     --do_Hres_ref 1
     --Href_resL 15.0
     --Href_resH 3.0
     --ctfstar NONE
     --estimate_B 1
     --B_resL 20.0
     --B_resH 3.0
     --apix "Pixel size" * 2.0

     if Volta Phase Plate, add:

     --phase_shift_L 10
     --phase_shift_H 175
     --phase_shift_S 10
     --phase_shift_T 1
     --defL 3000
     --defH 12000
     --defS 500
     --astm 3000
     --bfac 100
     --resL 20.0
     --resH 3.0
     --boxsize 1024
     --refine_after_EPA 0
     --convsize 30
     --Href_bfac 50
     --do_validation 1
$def ul(data): $if data: