From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jun 17 2019 - 15:57:21 CDT

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,
>
> I‚**m trying to merge pdf‚**s and psf‚**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 ‚**merge‚** function I get the protein not as I see them after
> the ‚**moveby‚** 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/