Re: shift the molecules

From: Chris Harrison (
Date: Thu Aug 23 2012 - 22:38:51 CDT

You should be able to do this with segnames.

set sel1 [atomselect top "segname ASL AZL"]
$sel1 move by {0 0 5}
set selall [atomselect top all]
$selall writepdb moved5z.pdb
$selall delete
$sel1 delete

Does this not work?


On Thu, Aug 23, 2012 at 3:29 AM, oguz gurbulak <> wrote:
> I have two different types of molecules with segnames ASL and AZL. And I
> want to shift ASL and AZL molecules and change the positions of the
> molecules along the z axis in the simulation box for one record or every
> record when I load dcd file into the psf file. Is it possible to do it ?
> Could you please help me about this issue ? By the way I tried Dear Swarna’s
> method in previous mail to do it but I couldn’t do it with the segnames ASL
> and AZL.
> *********************
> set sel1 [atomselect top "protein"]
> $sel1 move by {0 0 5}
> it will move the selected molecule 5A in the Z direction.
> then set all [atomselect top all]
> $all writepdb modified.pdb
> hope this will help you.
> ********************
> Thanks for the help.
> Kind regards.

Chris Harrison, Ph.D.
NIH Center for Macromolecular Modeling and Bioinformatics
Theoretical and Computational Biophysics Group
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801       Voice: 773-570-6078                          Fax: 217-244-6078

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