VMD-L Mailing List

From: John H (johnhamre3_at_gmail.com)
Date: Mon Jun 17 2019 - 16:38:06 CDT

Thank you, John. That is exactly what I wanted to do. I'm using version
1.9.2, will upgrade.

Best,

John

On Mon, Jun 17, 2019 at 4:57 PM John Stone <johns_at_ks.uiuc.edu> wrote:

> Hi,
> Are you running VMD 1.9.3 or 1.9.4aXX ??
> If you're running the latest VMD 1.9.4 test versions, you can use a new
> command to build a new molecule from multiple selections, e.g.:
> mol fromsels $sel1 $sel2 $sel3 $sel4
>
> That will create a new VMD molecule from a list of atom selections that
> reference other molecules. The new molecule will consist of the atoms
> from each of the listed selections, in order.
>
> Once the merged molecule is built, you can write it out as a PSF.
>
> Best regards,
> John Stone
> vmd_at_ks.uiuc.edu
>
>
> On Mon, Jun 17, 2019 at 01:50:19PM -0700, Bassam Haddad wrote:
> > It is because the merge function merges the .pdb & .psf, not the
> molecule
> > that you have loaded. Meaning, you have to write a new .pdb with the
> > updated coordinates before attempting to merge.
> > On Mon, Jun 17, 2019 at 10:05 AM John H <[1]johnhamre3_at_gmail.com>
> wrote:
> >
> > Hello,
> >
> > Iâ**m trying to merge pdfâ**s and psfâ**s but am having trouble. I
> have
> > been loading 2 proteins, using these commands;
> >
> > set sel [atomselect 0 all]
> >
> > $sel moveby {0 20 0}
> >
> > And get a nice image of the separated proteins. The problem is that
> when
> > I use any â**mergeâ** function I get the protein not as I see them
> after
> > the â**movebyâ** command, but together in the same space again. Does
> > anyone know a way around this? Thanks.
> >
> > References
> >
> > Visible links
> > 1. mailto:johnhamre3_at_gmail.com
>
> --
> 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/
>