ChimeraX Recipes

Make a helical filament atomic model

To make a helical filament three subunits long from a single subunit PDB 6g19 with rise of 46 Angstroms per turn and 76 degrees rotation per subunit I’ll use the ChimeraX sym command.

I want the axis of the filament aligned to the axis of the double stranded RNA, chains X and Y. To calculate this axis I open 2 copies of the structure, align the second copy RNA to the first copy RNA shifted by one nucleotide, then use the measure rotation command to get axis of the rotation that moves the first copy to the second copy.

open 6g19
open 6g19
align #2/X:1-13@P #2/Y:2-14@P to #1/X:2-14@P #1/Y:1-13@P 
measure rotation #1 to #2
sym #1 H,46,74,3 axis #3 copies true

Here is what this looks like:

6g19 helix

I colored the RNA blue with command

color #4/X,Y cornflowerblue

I changed the subunit colors using the color buttons in the Models panel.

Tom Goddard, September 10, 2020