[chimerax-users] Measuring pore diameter

[Elaine Meng]

Good day Tata Santosh Rama Bhadra Rao,

There is no tutorial for measuring pore diameter, sorry.  ChimeraX does not have a tool specifically to show a tunnel and report the pore radius -- if you wanted something like that maybe you would need to use other software like HOLE, MOLE, Caver, etc., maybe MolAxis. 
For example, here are MOLEonline and MolAxis servers:
<https://mole.upol.cz/>
<https://bioinfo3d.cs.tau.ac.il/MolAxis/>

However, if you are willing to choose two points yourself in ChimeraX, you can measure the distance between them.  Some possible approaches:

(1) You can measure the distance between any two atoms, e.g. show atoms, Ctrl-click to select first atom, Shift-Ctrl-doubleclick second atom, choose "Distance" from resulting context menu

(2) You can use the "tape measure" mouse mode to click and drag a measurement. This can be between atoms, ribbons, and/or surface points.  First you have to assign a button to this function and then use it, e.g. command

mouse right "tape measure"

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#mousemode>
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html#tapemeasure>

...and then right click-drag to do the measurements.

However, it can be very difficult to get to the positions you want to measure, especially if you are showing a tunnel surface.  You may need to use clipping such as with the Side View (menu: Tools... General... Side View) and even then it may not work the way you would like.  In that case you would need to use other software as mentioned above.

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


> On Jul 26, 2022, at 8:18 PM, SANTOSH RAMA BHADRA RAO TATA via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Good day Meng,
> 
> I'm trying to find the tutorial for the measuring the pore diameter. Can you please help me which protocol goes well with it. 
> 
> Thanking you,
> 
> With best wishes,
> Tata Santosh Rama Bhadra Rao,
> PhD Scholar,
> C/O Prof Helen Irving,
> La Trobe university,
> Bendigo, Vic-3550,
> Australia.
> Email: 19807877 at students.latrobe.edu.au; 
>             S.Tata at latrobe.edu.au
> Phone: 0499263974