VMD-L Mailing List

From: Jacob D Durrant (durrantj_at_pitt.edu)
Date: Wed Jun 21 2017 - 18:49:34 CDT

Hi guys. I ended up converting the trajectory to the pdb format and
reordering the atoms using some python code. Thanks for your help just the
same, though! All the best.

On Thu, Jun 1, 2017, 3:46 PM Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:

> Hi Jacob,
>
> there is no simple ways to swap the identity of atoms, but you can swap
> their coordinates, provided they have exactly the same number of atoms:
>
> proc swapcoords {selA selB} {
> set A [atomselect top "$selA"]
> set B [atomselect top "$selB"]
>
> set tmp_coords [$A get {x y z}]
> $A set {x y z} [$B get {x y z}]
> $B set {x y z} $tmp_coords
> }
>
> swapcoords "chain A" "chain B"
>
>
> Best,
> Jerome
>
> On 31 May 2017 at 17:37, John Stone <johns_at_ks.uiuc.edu> wrote:
>
>> 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!Â
>
>
>> > --
>> >
>> > 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/
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>>
> --

Sent from my mobile.