VMD-L Mailing List

From: Tran, Tran (TrTran_at_clarku.edu)
Date: Tue Sep 27 2016 - 20:18:31 CDT

Hi VMD users,

I'm currently working on two insulin molecules, one from simulations and other from x-ray. I have 8000 frames of the simulations one and 1 frame of the x-ray. I want to set the x-ray as reference, align them while running through all 8000 frames of the simulations molecule. I used the command "measure fit," but it created some problems. First, the command "measure fit" just align two molecule at a single frame, so when I change to the next frame, I need to realign them. Secondly, after aligning the two molecules, I saved it at a visualization file, however, they dont remain aligning when I reopen the file.

Do you know any tools that can help with molecule alignment and comparing the differences between them?

Thank you so much!!

-tran