VMD-L Mailing List

From: Samuel Flores (samuel.flores_at_yale.edu)
Date: Thu May 25 2006 - 21:02:47 CDT

Samuel Flores
Graduate Student
Gerstein Lab
 
Office:
Bass 437
266 Whitney Avenue
New Haven, CT 06520
203.432.5405
 
Home:
28 Pearl Street
New Haven, CT 06511
cell: 203.747.2682

-----Original Message-----
From: Samuel Flores [mailto:samuel.flores_at_yale.edu]
Sent: Thursday, May 25, 2006 9:08 PM
To: 'Samuel Flores'; 'John Stone'; 'Leyla Celik'
Cc: 'vmd'
Subject: number of frames in pdb file?

Hi Guys,

Is there a way to determine the number of frames in a file? I would like to
render each frame, then later make an animated gif. However to do that I
have to know the maximum frame number..

Thanks

Samuel Flores
Graduate Student
Gerstein Lab
 
Office:
Bass 437
266 Whitney Avenue
New Haven, CT 06520
203.432.5405
 
Home:
28 Pearl Street
New Haven, CT 06511
cell: 203.747.2682
-----Original Message-----
From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
John Stone
Sent: Thursday, May 25, 2006 3:54 PM
To: Leyla Celik
Cc: vmd
Subject: Re: vmd-l: rmsf

Hi,
  The "measure rmsf" command in VMD 1.8.4 only calculates the RMSF for
each atom independently and doesn't do any sort of summing of atoms in
groups. You could do this yourself in a Tcl script if you know what
you want. If what you really want is rmsd for these groups of atoms,
then use "measure rmsd" instead.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, May 24, 2006 at 01:07:55PM +0200, Leyla Celik wrote:
>
> Hi,
>
> I want to calculate the rmsf fluctuation for groups of atoms (aminoacid
> groups). Is this possible and if so how do I implement it in Tcl?
> If it is not possible to do for groups of atoms I would also like some
> help impelementing if for sigle atoms.
>
> Thanks
>
>
> --
> Leyla Celik
> Kemisk Institut
> Aarhus Universitet
> Langelandsgade 140
> 8000 Århus C
> Danmark
> Tlf: +45 8942 3869
> e-mail: lc_at_chem.au.dk 

-- 
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