Re: Transferring bond list to new molecule

From: Mert Gür (gurmert_at_gmail.com)
Date: Wed Dec 17 2014 - 18:06:05 CST

Thanks Josh!

It worked.

I actually was hoping there is some keyword (similar to name) that I can
comcat later; so that I can set it at once for all replicas. Now I guess I
have to change the index/numbering in the bond list to define the bonds for
each replica.

I guess I got mixed up about the mailing lists last night. You are correct,
It is a VMD-L question.

I am writing the last/subsequent step just for the sake of completeness of
the documentation in the mailing list:

topo setbondlist $bl -molid 1

Best,

Mert

On Wed, Dec 17, 2014 at 6:18 AM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:
>
> Technically a vmd-L question, but see the documentation for topotools for
> your answer (
> http://www.ks.uiuc.edu/Research/vmd/plugins/topotools/#TOC-getbondlist-type-order-both-none-).
> Basically it would be something like:
>
> set bl [topo getbondlist none -molid 0]
> topo setbondlist none -molid 1
>
> -Josh Vermaas
>
> On 12/16/2014 11:17 PM, Mert Gür wrote:
>
> Dear all,
>
> I just can't find the keyword that I am looking for. I am trying to
> transfer the bond list of a molecule (ID 0) to its replica that I have
> generated (ID 1).
>
> In other words I would like to make the following operation for a bond
> list instead of atom names;
>
> set p [atomselect 0 all]
> set pn [$p get name]
>
> set a [atomselect 1 all]
> $a set name $pn
>
> Thanks,
>
> Mert
>
>
>

-- 
Dr. Mert Gür,
Joint Center for Artificial Photosynthesis
Lawrence Berkeley National Laboratory
Office 1: JCAP, 2929, 7th Street, Berkeley, 94710
Office 2: 260F Stanley Hall, UC Berkeley, Berkeley, CA 94720-3220
Email: mgur_at_lbl.gov, mgur_at_berkeley.edu
Telephone: +1 510 666-2745

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