VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Thu Jan 09 2020 - 04:43:56 CST

Perhaps you can use TCL's capabilities to browse through your "Sequence
space" detect the patter - get the residue numbers against the pattern and
use that to create a representation.

The atomselection language within VMD should help with that. The sequence
search will have to be something that you would want to program -- but
simple string searching should suffice.

Roughly it should look like this.

1) Select DNA
2) Get sequence (in single letters as a string)
3) Search for pattern
4) Map back to original array of residues holding residue numbers
5) Pass residue numbers to selection for visualization.

Hope this helps. Otherwise write back.

On Thu, Jan 9, 2020 at 4:54 PM Dominique Mias-Lucquin <
dominique.mias-lucquin_at_loria.fr> wrote:

> Hi,
> My aim is to find and display a sequence pattern in a DNA strand, like
> 'sequence "C..C"' for protein.
> It could be done externally, then reported in VMD, I just hoped that it
> was possible to do it all in VMD.
> Thanks a lot for the answer,
> Dominique MIAS.
>
> ----- Mail original -----
> > De: "John Stone" <johns_at_ks.uiuc.edu>
> > À: "Dominique Mias-Lucquin" <dominique.mias-lucquin_at_loria.fr>
> > Cc: "vmd-l" <vmd-l_at_ks.uiuc.edu>
> > Envoyé: Mardi 7 Janvier 2020 21:15:51
> > Objet: Re: vmd-l: Select Nucleic Acid sequence
>
> > Hi,
> > There isn't currently a sequence-based selection in VMD itself,
> > but if you load the structure into the Multiseq plugin, you should be
> > able to load in sequences, perform alignments, and then use the resulting
> > "conserved residues" to generate a selection in VMD. This is indirect at
> > best, but that's all that exists that's built-in presently.
> >
> > What you're asking for would be a special combination of sequence search
> plus
> > atom seletion in a single step, but it's an unusual need vis a vis
> > typical VMD use cases.
> >
> > What are you doing that leads you to want to select by sequence?
> > Maybe there's another approach that would be more direct if you
> > tell us more about what you're doing.
> >
> > Best,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Fri, Dec 20, 2019 at 02:37:15PM +0100, Dominique Mias-Lucquin wrote:
> >> Hello,
> >> I am currently working on nucleic acid, and I was wondering if there
> is a
> >> way to select DNA/RNA by sequence ?
> >> Thank you in advance,
> >> Dominique MIAS.
> >
> > --
> > 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/
>
> 

-- 
Best,
/A