How to View Nanobody Molecular Dynamics in ChimeraX

Tom Goddard
March 15, 2021

Here is one of the MD trajectory files from James Lincoff from Micheal Grabe's lab production_Nb6cRBD1.pdb.

Opening the trajectory

To open a molecular dyanmics trajectory of a nanobody bound to the SARS-CoV-2 receptor binding domain use the ChimeraX open command with the "coordset true" option:

      open ~/Downloads/production_Nb6cRBD1.pdb coordset true

A bug introduced in ChimeraX on Feb 17, 2021 makes this not work, so user a ChimeraX daily build older than that, or ChimeraX 1.1. You ChimeraX version is listed at the top of the Log panel.

Trajectory playback

To play through the trajectory use the slider or use the command

      coordset #1 1,9951,50

This says to play frames 1 to 9951 stepping 50 frames at a time. The file only contains every 50th frame.

Movie recording

To record a movie playing the frames use command sequence:

      movie record ; coordset #1 1,9951,50 ; wait 200 ; movie encode ~/Desktop/nanobody_rbd.mp4

The record button on the slider won't work well because it plays every frame even though the file only contains every 50th frame, so the movie plays only one new frame every 2 seconds. We are working on fixing this.