VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Nov 17 2004 - 11:17:10 CST

Hi,
  If you still need help with this, it would be useful to get a transcript
of the exact alignment commands you are performing, along with a copy of
the structure file(s) you're working with, otherwise it's quite difficult
for anyone to provide you with any suggestions to solve your problem.
You can email them to me, no need to send them to all of VMD-L.

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Nov 11, 2004 at 11:04:01PM -0500, Laura Lucan 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
> > 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078