From: John Stone (
Date: Mon Sep 26 2005 - 10:26:59 CDT

  You can use the atomselect "move" subcommand to apply an arbitrary
4x4 transformation matrix to the atom coordinates in a selection. Using
this, you should be able to perform any transformations you want. I don't
know if that's what you're looking for when you say "clear" and "elegant",
but the process just involves doing something like this (replace the
matrix with one that's not an identity matrix...):
  set sel [atomselect top "protein"]
  set matrix { { 1 0 0 0 }
               { 0 1 0 0 }
               { 0 0 1 0 }
               { 0 0 0 1 } }
  $sel move $matrix

As you can see, you can apply any transformation to any part of your
structure just by making different selections and matrices for each
of the parts you're interested in separately transforming.

  John Stone

On Mon, Sep 26, 2005 at 04:35:10PM +0200, andrea spitaleri wrote:
> Hi all,
> this is my first post to mailing list. I am using vmd for my MD
> visualization and I found it very nice program.
> Now, I have been trying to setup my system in a proper way using vmd.
> The system is protein + membrane.
> My aim is to put the protein above the membrane, and tilt it with an
> angle ALPHA respect to the Z-axes of the protein itself.
> I have used the package Orient to rotate the protein and moving it "by
> hand" I almost get what I want.
> However, I am wondering if there is a "clear" and "elegant" way to
> achieve this job.
> any suggestion are welcome.
> thanks
> regards
> andrea
> --
> -------------------------------
> Andrea Spitaleri
> Dulbecco Telethon Institute

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