Tools and notes

Here is a collection page for scripts and toolkits used for handling NMR/X-ray crystallography/cryoEM data.

CryoEM — Relion 3

Rescale pixel size and box size:

relion_image_handler --angpix 1.0 --rescale_angpix 1.5 --new_box 200 --i input.mrc --o output.mrc

Generate particle stack:

relion_preprocess --operate_on Extract/jobxxx/particles.star --operate_out new_name (OUTDATED)
relion_stack_create --i Polish/job125/shiny.star --o shiny-all --one_by_one
(one_by_one argument to save one image at one time, otherwise it will operate in memory and crash if memory space is not enough)

Edit (remove/add) RELION’s star file

relion_star_handler --i xx_yy.star --remove_column rlnGroupName --o xx_yy_no_groupname.star

Relion reconstruct a map

mpirun -n 20 `which relion_reconstruct_mpi` --i input shiny.star --o relion.mrc --sym C1 --angpix 0.87 --mask_diameter 150 --fsc 

ChimeraX

Remove dust in map: surface dust #

Remove water in PDB: delete #2:HOH

Write a movie with fixed width, length, rocking angles: movie record; size 400,400; turn y 360 rock 3600; wait 300; movie encode ~/Desktop/movie_y_360.mp4 quality high

Select ligand, residues in PDB: Select #1:ADP

Select atom in PDB: Select #1:Mg

Color ligand, residues in PDB: Color #1:ADP yellow

Color water in PDB:color #2:HOH yellow

fit pdb (#2) to another pdb(#1) (or map to map):  fit #2 in #1

fit map/pdb (#2) to another map(#1):  fit #2 inMap #1

Save image: save image XXX.png transparentBackground true pixelSize 0.1
(the smaller, the large image (0.1 gives ~1 MB)

Scale volume threshold : volume multiply #2 scaleFactor 10

Morph maps: volume morph #5, 1, 2,3,4
(#5 is new map generated with morphing, 1,2,3,4 are maps to be morphed in sequence)

Color in specified sequential colors: color sequential #4/C palette “red:orange:blue:green:yellow:indigo:violet”
(color sequential “object” palette “colors separated by colon”)

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out /  Change )

Google photo

You are commenting using your Google account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s