• Outreach

From: Ashar Malik (asharjm_at_gmail.com)
Date: Fri Sep 23 2016 - 06:40:58 CDT

Hi,

The calculation of the angles is not the difficult bit here. Its what you
need to calculate the angle between. A dihedral angle is NOT the same as
the angle. The two concepts are very different. Perhaps a better way of
analysing this would be to first understand how the two segments of the
protein move about one another. Are they moving in the same plane, or in
different planes - or a mix of both.

The angle measurement comes out fairly easily once you have points that
define your system. 3 in case you decide on taking an angle and 4 in case
of a dihedral. Once you have those points the rest should be quite simple
by either using

- measure command (either in angle or dihed mode) with fake atoms which
define your points see here for use of measure with angle and dihed:
https://www-s.ks.uiuc.edu/Research/vmd/vmd-1.9.1/ug/node136.html with
the measure command you need to provide indexes of the atoms ... so its
perhaps easiest to write the coordinates of your selected points (again 3
if you want to measure the angle and 4 if you want to measure the dihedral)
to a pdb like file and load that into VMD. With just the 3 or 4 points now
loaded into your top molecule in VMD -- just running the commands below
should give you what you need.

- measure angle [[atomselect top all] get index] for this to work you
must have only and exactly(!!!) 3 atoms otherwise make a selection of 3
only and replace [atomselect top all] with that.
- measure dihed [[atomselect top all] get index] for this to work
you must have only and exactly(!!!) 4 atoms otherwise make a
selection of 4
only and replace [atomselect top all] with that

- or using the coordinates of your points and doing some maths with it
-- see here http://www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node163.html
for
functions to accomplish this.

Hope this helps.

Best,
/A

On Fri, Sep 23, 2016 at 10:18 AM, Felicia Jiang <feliciahjiang_at_uchicago.edu>
wrote:

> Hi,
>
> I am trying to measure the angle between two domains of a protein that
> opens and closes. I have seen previous posts that mention using measure
> inertia to calculate the angle between two principal axes. However I am
> trying measure the dihedral angle between the two planes (the two domains)
> of the protein. Is there a script that does this or can you suggest a
> better approach? Thanks.
>
> Best,
> Felicia
>

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Best,
/A
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