ChimeraX version: 1.9

example: PDB 3OWI

1. Load the structure, setup the style, and split the chains.

   open 3owi
   set bgColor white
   lighting simple
   graphics sil true width 1 color black
   nucleotides atoms
   ~hbonds
   split #1
   log chains #1

2. Save the domain residues and color the domains (see available colors t build-in colors).

   name P1 #1:1-7, 84-88
   name P2 #1:12-28
   name list
   color #1 gray
   color P1 gold
   color P2 blue
   color ligand cyan
   color ions tomato

3. Setup the transparency.

   surf ligand
   surf style solid
   trans #1 70 All
   sel zone ligand 7 nucleic
   graphics sel col gold width 2
   color sel lime
   trans sel 0 All
   trans ligand 0 All
   trans ions 0 All

4. Create the camera view and save the results.

   turn x 60
   view sel; zoom 1.7
   view name pocket
   view; zoom 1.4
   ~sel
   save test.png transparentBackground true pixelSize 0.03 supersample 3

The result of test.png:

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