[Chimera-users] how to find size of a molecule using Chimera

[Elaine Meng]

Hi Aditi,
You can measure distance between any two atoms, e.g. Ctrl-click first atom to select, Shift-Ctrl-doubleclick to select second atom and choose "Show Distance" from the pop-up menu.  Other ways to do this are with "distance" command or "Distances" tool
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#distances>
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html>

Or maybe you want to measure on the spacefilling representation or molecular surface instead of the atom surfaces. In that case you would have to show the surface, put markers (fake atoms) on the surface, and then measure distance between the fake atoms.

(1) show surface: Select the molecule (e.g. with Select menu or Ctrl-click on atom and press the up arrow key on keyboard to expand to whole molecule), show its surface (e.g. menu: Actions... Surface... show)

(2) put markers on surface: start Volume Tracer (in menu under Tools... Volume Data).  In Volume Tracer dialog, use Mouse menu to "place markers on surfaces" and in the dialog specify which button you are going to use to place markers.  Use that button to put markers on the surface on the two points you want to measure between.
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html>

(3) measure distance between markers as described above for atoms.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Oct 10, 2022, at 7:43 AM, Aditi Laddha via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi Elaine,
> 
> I wanted to find the size of a molecule which acts as a substrate (consisting of multiple elements) for my protein, I want to know the diameter of the molecule. But I am unable to find a way to do it.  Can you please guide me through the process of determining the size of a molecule? 
> 
> -- 
> Regards,
> Aditi Laddha
> PhD Scholar
> Indian Institute of Technology,
> Kanpur, Uttar Pradesh 208016