• ## Outreach

From: vitalini_at_zedat.fu-berlin.de
Date: Wed Aug 22 2012 - 10:21:23 CDT

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!