Masking for Local Refinement

volume gaussian #1 sDev 2
volume resample #4 onGrid #1

Opening Files

Open a PDB:

open 4JIX

Open an EM map:

open emdb:25658

Map Manipulation

Z-flip a volume:

volume flip #1

Invert contrast for tomogram:

volume scale #1 factor -1

Hide small disconnected regions (dust):

surface dust #1 size 10

Change window size:

windowsize 500 500

Region Focus and Visualization

Focus on one region and fog background:

camera ortho
lighting depthCue true

Change helices to cylinders:

preset cylinders

Side Chain Density Display

surface zone #2 near #1/A:404-441
color byhetero
volume #2 subdivide true subdivisionlevels 2

Coloring

Color map by nearby model:

color zone #1 near #2 dist 3

Color atoms by element:

color O red
color N darkblue

Map Orientation

Orient and clip:

view clip false orient
turn z 90
clip
clip near 5

Saving Structures

Save PDB of selected model only:

save /path/to/test.pdb selectedOnly true relModel #3

Scene Settings

Set lighting and silhouette:

light soft
graphics silhouettes true width 1

Make the map transparent:

transparency 95 target s

Assign Secondary Structure

Assign helix or beta sheet:

setattr r isHelix true :1-10.a,23-36.b
setattr r isSheet false :1-10.a,23-36.b

Selection and Deletion

Delete everything except the selected region:

del ~sel

Select chains A–D:

sel /A-D

Select multiple specific chains:

sel #6/BV/BO

Make cartoon thicker:

cartoon style width 3 thick 3

Low-pass filter a map:

surface resolution 10

Create a base mask using Gaussian filter:

volume gaussian #1 sDev 2

Mask a map using a surface:

volume mask #3 surface #4 fullMap true

Zone around one part of the map and save as new map:

volume zone #6 nearAtoms #3 range 20 newMap True minimalBounds True

Match map #5 to #3/C:

mm #5 to #3/C

Combine models into one:

combine #2,4,5 modelId 7 name 512combine.pdb

Movie Making

Make movie going through tomogram slices

movie record
volume #2 plane z,84,338
wait 264
volume #2 plane z,338,84
wait 264
movie encode ~/Desktop/tomogram.mp4 quality high