VMD-L Mailing List

From: Justin Gullingsrud (justinrocks_at_gmail.com)
Date: Fri Nov 12 2004 - 00:28:22 CST

Laura,

You need to manually pick three our of the four Fe atoms in the first
molecule to use in the atom selection. How you pick them is up to
you, but there has to be the same number as in the second selection.
You also need to make sure that the Fe and S atoms are in the same
order in both selections. If that's not the case then you'll need to
go and manually reorder the lines in the pdb file to make this so,
otherwise VMD will align an Fe atom with an S atom, which isn't what
you want.

Cheers,
Justin

On Thu, 11 Nov 2004 23:04:01 -0500, Laura Lucan <laura.lucan_at_comcast.net> wrote:
> I did, but is so much not working:-(
> As long as I keep counting Fe4S4 resp. Fe3S4, I get the same error message.
> Is there any other way than atomselect?
> Thank you very much for your reply.
> Laura.
>
>
> ----- Original Message -----
> From: "Luis Gracia" <lug2002_at_med.cornell.edu>
> To: "Laura Lucan" <laura.lucan_at_comcast.net>
> Cc: <vmd-l_at_ks.uiuc.edu>
> Sent: Thursday, November 11, 2004 8:24 PM
> Subject: Re: vmd-l: VMD newbie question
>
> > Laura Lucan said the following on 11/11/04 17:18:
> >> Hello,
> >> I need to align two pdb protein structures upon Fe-S clusters,
> >> unfortunately with different number atoms...and of course it's not
> >> working :-(
> >> Any advice or link to documentation is welcome.
> >> Thank you.
> >
> > Hi,
> >
> > you could try any other combination of selection that does not rely on
> > resid. Like resname, name, type,...
> >
> > good luck
> >
> > Luis
> >
> > --
> > Luis Gracia, PhD
> > Department of Physiology & Biophysics
> > Weill Medical College of Cornell University
> > 1300 York Avenue, Box 75
> > New York, NY 10021
> >
> > Tel: (212) 746-6375
> > Fax: (212) 746-8690
> > lug2002_at_med.cornell.edu
> >
> 

-- 
The spirit of Plato dies hard.  We have been unable to escape the
philosophical tradition that what we can see and measure in the world
is merely the superficial and imperfect representation of an
underlying reality.
                -- S.J. Gould, "The Mismeasure of Man"