From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed May 31 2017 - 16:37:47 CDT

Hi Jacob,
  This isn't a built-in feature of VMD. You'd either need to write new C/C++ code
to do this, or do it in a script of some sort. None of the obvious options
for implementing this are very elegant unfortunately.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, May 14, 2017 at 12:28:32AM +0000, Jacob D Durrant wrote:
> 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!
> --
>
> Sent from my mobile.

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/