VMD-L Mailing List
From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Sat Apr 12 2014 - 05:49:13 CDT
Norman's simple solution does not work as the problem is in measure fit ...
I will probably have to make a routine along the lines Josh suggested ... I was thinking about this but I still hoped it can be done easier . Dont get me wrong, Josh's procedure is not difficult, but in my case this is a small part of a large modeling procedure and I hoped for an easy solution ...
Sent from my android device.
From: Norman Geist <norman.geist_at_uni-greifswald.de>
To: 'Vlad Cojocaru' <vlad.cojocaru_at_mpi-muenster.mpg.de>
Cc: VMD Mailing List <vmd-l_at_ks.uiuc.edu>
Sent: Fri, 11 Apr 2014 4:20 PM
Subject: AW: vmd-l: how to control the superposition (measure fit) ?
Does something like this work?
set a [atomselect 1 "resid 1 2 3"]
set b [atomselect 2 "resid 10 9 8"]
$a transaxis [measure fit $a $b]
> -----Ursprüngliche Nachricht-----
> Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im
> Auftrag von Vlad Cojocaru
> Gesendet: Freitag, 11. April 2014 14:16
> An: VMD list
> Betreff: vmd-l: how to control the superposition (measure fit) ?
> Dear all,
> I have a rather simple question but for which I did no figure an answer
> yet ... I have 2 DNA molecules which I want to superimpose.
> The superposition should be done like this:
> res 1 from mol 1 on res 10 from mol 2,
> res 2 from mol 1 on res 9 from mol 2,
> res 3 from mol 1 on res 8 from mol2,
> .. and so on ...
> If I do the selections "resid 1 to 3" and "resid 10 to 8", it does not
> work as VMD tries to superimpose 1 on 8, 2 on 9, and 3 on 10.
> I also tried to change the residue numbers in mol 2 such as res 10
> becomes res 100, res 9 becomes res 101, res 8 becomes res 102 (to have
> ascending order). However, still no success, VMD does not care about
> residue number, it still tries the same. ...
> Do I need to change all atom indices to actually make VMD superimpose
> the way I want ? Or is there an easier solution to this ?
> Thanks for any advice ..
> Best wishes
> Dr. Vlad Cojocaru
> Computational Structural Biology Laboratory
> Department of Cell and Developmental Biology
> Max Planck Institute for Molecular Biomedicine
> Röntgenstrasse 20, 48149 Münster, Germany
> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
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