Useful EMAN2 Commands
Published:
1. Check Movie or Micrograph Information
e2iminfo.py -H micrograph.mrc
2. Convert MRC to TIF
e2proc2d.py input.mrc output.tif
3. Convert Multiple MRC Files into TIFs
e2proc2d.py *mrc @tif
4. Scale a Map
e2proc3d.py input.hdf output.hdf --clip=140,140,140 --scale=2.8
5. Generate Random Projections of a Map
e2project3d.py map.mrc --outfile=proj.mrcs --orientgen rand:n=10:phitoo=1:trans=4
6. Low-Pass Filter a Map
e2proc3d.py input.mrc output.mrc --process filter.fourier:curres=3.5:targetres=7:dampamp=1:randomizephase=0
7. Sharpen a Map
e2proc3d.py input.mrc output.mrc --process filter.autosharpening:cref=1:mapres=2.5:lpfile=fsc.txt.fit
8. Calculate Structure Factor Curve of a Map
e2proc3d.py input.mrc output.mrc --calcsf output_sf.txt
9. Match Structure Factor Curve to Another Curve
e2proc3d.py input.mrc output.mrc --apix 1.08 --setsf sf.txt
10. Match Filtering Level of Another Map
e2proc3d.py input.mrc output.mrc --apix 1.08 --matchto other.mrc
11. Generate Random 2D Projections from a 3D Map
e2project3d.py map.mrc --outfile=projections.mrcs --orientgen random:n=1000:phitoo=1:inc_mirror=1:trans=10
12. Rotate a Map
e2proc3d.py input.mrc output.mrc --rot az,alt,phi
e2proc3d.py input.mrc output.mrc --rotspin n1,n2,n3,angle
13. Rotate Octahedral Map from 4-Fold View to 3-Fold View
e2proc3d.py input.mrc output.mrc --oct4fto3f
e2proc3d.py input.mrc output.mrc --rot 45,54.7356,0
14. Flip Handedness of a 3D Map
e2proc3d.py input.mrc output.mrc --process xform.flip:axis=o
15. Y-Flip a 3D Reference
e2proc3d.py input.mrc output.mrc --process xform.flip:axis=y
16. Apply Mask to a Map
e2proc3d.py input.mrc output.mrc --process mask.file:file=mask.mrc
17. Apply Cylindric Mask to a Map
e2proc3d.py input.mrc output.mrc --process mask.cylinder3d:innerradius=10A:outerradius=20A:length=60A:masksoft=10A
18. Simulate a Cylinder
e2proc3d.py :96:96:96:1 output.mrc --apix 1 --process mask.cylinder3d:innerradius=10A:outerradius=20A:length=60A:masksoft=10A
19. Simulate a Spherical Mask with RELION
relion_mask_create --denovo --box_size 256 --inner_radius 0 --outer_radius 50 --angpix 1.6 --o mask.mrc
20. Make a Mask Based on Threshold
e2proc3d.py input.mrc output.mrc --process mask.auto3d:nshells=5:nshellsgauss=5:thresh=3
21. Refine and Apply Helical Symmetry
e2proc3d.py input.mrc ouput.mrc --process xform.helical:apix=1.1:az0=22:z0=37.2:cdsym=c6:verbose=1:rstep=1
22. Apply Helical Symmetry Without Refinement
e2proc3d.py input.mrc ouput.mrc --process xform.helical:apix=1.1:az0=22:z0=37.2:cdsym=c6:verbose=1
