VMD-L Mailing List

From: Jacob D Durrant (durrantj_at_pitt.edu)
Date: Sat May 13 2017 - 19:28:32 CDT

Is it possible to reorder the atoms of a selection prior to output? Let me
explain my scenario.

I have simulated a protein that is a trimer. Let's say it has chain IDs A,
B, and C. There's a pocket at the interface of each monomer. So pocket AB,
BC, and CA. I saved the timer trajectory as three different trajectories
containing the alpha carbons of all protein atoms, as well as all the atoms
of the binding-pocket residues. My hope is to concatenate these three
trajectories and align them by the alpha carbons. I'll then cluster based
on the binding-pocket atoms.

But to align the concatenated trajectory in VMD, I need to reorder the
chains so they line up across the three monomeric trajectories. For pockets
AB and CA to line up, for example, I need to align the alpha carbons of
chain A to those of chain C, and the alpha carbons of chain B to chain A.
But that would require me to reverse the order of chain C and A in the
second trajectory.

I hope this makes sense. Thanks for your help! 

-- 
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