VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jan 07 2020 - 14:15:51 CST

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/