[Chimera-users] how to calculate the core diameter of a trimer (the individual subunits of this trimer is a helix)

[Elaine Meng]

Hi Ashok,
It depends on how "core diameter" is defined.  I searched for "coiled-coil" together with "core diameter" and found it once in a 2004 paper, but no specific definition was given.  It was probably meant as a general description rather than a specific measurement, i.e. several different measurements would show the general property of an  expanded core: you would just need to apply the same measurement to different trimer structures in order to compare them.

In Chimera, possibilities are to

(a) measure any atom-atom distance, for example between an alpha-carbon in one helix and the closest alpha-carbon in another helix. For example, Ctrl-click to select one atom, Shift-Ctrl-doubleclick to select the second atom and choose "show distance" from the resulting context menu.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#distances>

(b) use Axes/Planes/Centroids (in menu under Tools… Structure Analysis) to calculate a separate axis for each helix based on its backbone atoms and then measure pairwise axis-axis distance.  Each axis is shown as a cylinder.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes>

(c ) use Axes/Planes/Centroids to calculate one axis for all three helices together based on all their backbone atoms, with the option to set axis radius based on average axis-atom distance (diameter = 2x radius).  For example:
command: open 1coi
command: sym
Menu: Presets… interactive 2 (all atoms)
command: select protein & @n,ca,c,o
Menu: Tools… Structure Analysis… Axes/Planes/Centroids
… then choose to define axes.  
In the Define Axes dialog, choose the "selected atoms/centroids" option with "Replace existing axes" and "Radius: average axis-atom distance", Apply.  Then see what radius is reported in the Structure Measurements table (in this case 6.9 Angstroms, so diameter measured in this way would be 13.8 angstroms).

The third one sounds closest to what I think of as a diameter, but these are just guesses as how to to measure it.  If you have some specific definition, use that instead. I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Apr 20, 2014, at 12:10 PM, ashok rout <ashok9869 at gmail.com> wrote:

> Hi,
>  I have a transmembrane domain of a protein (20 amino acid long, single helix). The NMR derived structure comes out as a coiled-coil trimer. So can you please assists me how to calculate the core diameter of this trimer.
> Regards,
> Ashok