VMD-L Mailing List

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Mar 31 2014 - 00:35:37 CDT

Hi,

I guess it would also be possible, and quite easy to script, to use "measure
fit" with two atomselections. This, if I remember correctly, will return a
transformation matrix that you can easily apply to a 3rd atomselection
containing "all" of one of the molecules by doing something like:

set sel1 [atomselect top "resid 1 to 10"]
set sel2 [atomselect 1 "resid 200 to 210"]
set all [atomselect 1 "all"]
$all transaxis [measure fit $sel1 $sel2]
$sel1 delete
$sel2 delete
$all writepdb "aligned.pdb"
$all delete

!!! Untested but should show how it works ;)

Norman Geist.

> -----Ursprüngliche Nachricht-----
> Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im
> Auftrag von Ivan Gregoretti
> Gesendet: Freitag, 28. März 2014 22:57
> An: Hailin Huang
> Cc: vmd-l_at_ks.uiuc.edu
> Betreff: Re: vmd-l: Align specific residues of two structures
>
> Yes, there is, with one of VMD's plugins.
>
> Multiseq
> https://www-s.ks.uiuc.edu/Research/vmd/plugins/multiseq/
>
> Elijah Roberts, John Eargle, Dan Wright, and Zaida Luthey-Schulten.
> MultiSeq: Unifying sequence and structure data for evolutionary
> analysis.
> BMC Bioinformatics, 2006, 7:382.
>
> The user guide shows you how to use via a graphical user interface. It
> may be difficult to run at the command line but I would be delighted
> to be proved wrong by somebody in the list.
>
> Cheers,
>
> Ivan
>
>
>
> Ivan Gregoretti, PhD
> Bioinformatics
>
>
>
> On Fri, Mar 28, 2014 at 4:37 PM, Hailin Huang <hailin.huang_at_my.liu.edu>
> wrote:
> >
> > Dear Users,
> >
> > Is there a way I can align two protein structures at specific
> residues that are numbered differently? For example, how do I align
> residues 20-80 in structure A with residues 100-160 in structure B?
> >
> > Thanks,
> >
> > Hailin Huang 

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