[chimerax-users] Measuring pore diameter

[SANTOSH RAMA BHADRA RAO TATA]

Good morning Meng,

Thank you very much for the response will use the suggestions to get details from 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

________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Thursday, 28 July 2022 2:22 AM
To: SANTOSH RAMA BHADRA RAO TATA <19807877 at students.latrobe.edu.au>
Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
Subject: Measuring pore diameter

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://mole.upol.cz>>
<https://bioinfo3d.cs.tau.ac.il/MolAxis/<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/commands/ui.html#mousemode>>
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html#tapemeasure<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
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