Common questions when using FragBEST-Myo#

1. What if I have skeletal myosin instead of cardiac? Should I make any modifications to the code in the tutorial?#

Answer: You can follow Tutorial 3 as outlined. However, the key modification you need to make is ensuring that the pocket center is correctly defined. Since the reference structure (cardiac myosin) might not be suitable for skeletal myosin, you will need to use the first frame (frame 0) of your trajectory to define the pocket center and align the trajectory accordingly.

Here’s what you need to do (also mentioned this within hint in Tutorial 3):

  1. Use the first frame of your trajectory to identify the pocket center.

  2. Align the entire trajectory to the first frame to ensure consistency.

This adjustment ensures that the analysis is tailored to skeletal myosin or any other isoform you are working with.

2. I have other chains in the trajectory (not just the myosin heavy chain), should I remove them?#

Answer: It depends.

If those chains are relevant to or close to your region of interest (pocket), you should keep them to preserve the original local environment and ensure accurate analysis.

However, if those chains are far away from your pocket region and do not interact with it, it is recommended to remove them to reduce computational cost and simplify the analysis. This can help streamline the workflow without compromising the accuracy of results.