From: Dominique Mias-Lucquin (
Date: Thu Jan 09 2020 - 02:28:07 CST

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" <>
> À: "Dominique Mias-Lucquin" <>
> Cc: "vmd-l" <>
> 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
> 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.
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