VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Aug 28 2012 - 16:13:09 CDT

Hi,
  If you look at the orient page, the author notes that you can
access the principal axes within the "I" variable in his example,
for purposes other than drawing:
  http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/orient/

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Aug 22, 2012 at 05:21:23PM +0200, vitalini_at_zedat.fu-berlin.de wrote:
> Dear VMD people,
> I need to calculate the axis of a alpha-helix. Looking at your mailing
> list I found this script
> http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/orient/
> which I have followed, but I don't understand the output, which would look
> like
>
> Calculating principal axes.
> Getting the center-of-mass...
> Total weight: 3766.921927213669
> Computing the inertia tensor...
> Drawing the principal components...
> Total weight: 3766.921927213669
> cone {-91.62954945869689 -62.57318843465899 -48.747545205836516}
> {-90.97943044332558 -62.573187875234254 -56.518130967501435} radius
> 1.949433536529541
> cone {-125.31236856684171 -62.573187756152116 -20.265678220661844}
> {-133.08295432850662 -62.57318702710066 -20.91579723603309} radius
> 1.9494335365295412
> cone {-94.2300228006925 -31.382254087885492 -17.665199686136347}
> {-94.2300221208201 -23.584519941767383 -17.66519906787622} radius
> 1.9494335365295412
> {0.08337281102292253 7.174196071756237e-8 -0.9965184265140966}
> {-0.9965184265140953 9.349529519907606e-8 -0.08337281102291569}
> {8.718845552497836e-8 0.9999999999999932 7.928715138746972e-8}
>
> which information corresponds to the axis? Sorry for the probably silly
> question, but I'm quite new to the use of vmd.
>
> In addition again in thesame post of the mailing list it was mentioned a
> script to calculate the angle between two of those axis. Unfortunately the
> document cannot be found
>
> /Research/vmd/mailing_list/vmd-l/att-2279/fit_angle.tc
>
> does anyone know if there is another script to do the same?
>
> Thanks! 

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