VMD-L Mailing List

From: Ahmet Bakan (abakan_at_ku.edu.tr)
Date: Mon May 31 2004 - 15:54:52 CDT

Hi John,

I have a single residue and I do not get any angles. I have solved the
problem with my script and attached the final version. I tested it on
decalanine, it works fine. I takes the indices of four atoms and frame
number.
Phi i1 i2 i3 i4 iFrame
There is also a loop to analyze a DCD file.

Thanks,

Ahmet
==========ABC==========
Ahmet Bakan
Chemistry, Junior
Koc University
abakan_at_ku.edu.tr
ICQ #86167698
http://home.ku.edu.tr/~abakan

-----Original Message-----
From: John Stone [mailto:johns_at_ks.uiuc.edu]
Sent: Monday, May 31, 2004 8:45 PM
To: Ahmet Bakan
Cc: 'VMD-L'
Subject: Re: vmd-l: Torsional Angles

Ahmet,
  Rather than writing your own script for this purpose, lets go back
to the original problem you were having, as I suspect some of the difficulty
originates there. Check ou the Ramachandran plot for the structure you're
interested in and let us know if you get the angles you expect. You can
type in atom selections in the ramaplot plugin to view just the angles
you're interested in. If you still get unusual angles, then I may want
to get a copy of the structure file you're loading that's exhibiting
the strange results.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, May 31, 2004 at 03:41:49AM +0300, Ahmet Bakan wrote:
> Dear All,
>
>
>
> I have written a short procedure which takes four indices as input and
gives
> out dihedral angle.
>
> For phi angle I enter corresponding indices C'-N-Ca-C'
>
> For psi angles I enter corresponding N-Ca-C'-N indices
>
> I have checked the proc on decalanine and did not get the right phi or psi
> values for any residue.
>
> What may have been wrong?
>
> I appreciate any suggestions,
>
> Ahmet
>
> ==========ABC==========
>
> Ahmet Bakan
>
> Chemistry, Junior
>
> Koc University
>
> abakan_at_ku.edu.tr
>
> ICQ #86167698
>
> http://home.ku.edu.tr/~abakan
>
>
>
> _____
>
> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf
Of
> Ahmet Bakan
> Sent: Wednesday, May 26, 2004 9:53 PM
> To: VMD-L
> Subject: vmd-l: Torsional Angles
>
>
>
> Hi All,
>
>
>
> I want to retrieve phi and psi angles from this single residue along a
> trajectory. What I get is 0 value using the following lines:
>
> set ALL [atomselect top "all"]
>
> $ALL get {psi}
>
> $ALL get {phi}
>
>
>
> What may be the problem?
>
>
>
> Thanks,
>
> Ahmet
>
>
>
> ==========ABC==========
>
> Ahmet Bakan
>
> Chemistry, Junior
>
> Koc University
>
> abakan_at_ku.edu.tr
>
> ICQ #86167698
>
> http://home.ku.edu.tr/~abakan
>
>
> 

-- 
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

  • application/octet-stream attachment: phi.tcl