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Good morning Meng,</div>
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Thank you very much for the response will use the suggestions to get details from it. </div>
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<span style="font-family:"Times New Roman",Times,serif; font-size:12pt; line-height:normal"></span><span style="font-family:"Times New Roman",Times,serif; color:rgb(12,100,192); font-size:12pt; line-height:normal">Tata Santosh Rama Bhadra Rao,</span></div>
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S.Tata@latrobe.edu.au</span><wbr style="display:inline-block"></a></div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Sent:</b> Thursday, 28 July 2022 2:22 AM<br>
<b>To:</b> SANTOSH RAMA BHADRA RAO TATA <19807877@students.latrobe.edu.au><br>
<b>Cc:</b> ChimeraX Users Help <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> Measuring pore diameter</font>
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<div>Good day Tata Santosh Rama Bhadra Rao,<br>
<br>
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. <br>
For example, here are MOLEonline and MolAxis servers:<br>
<<a href="https://mole.upol.cz">https://mole.upol.cz/</a>><br>
<<a href="https://bioinfo3d.cs.tau.ac.il/MolAxis">https://bioinfo3d.cs.tau.ac.il/MolAxis/</a>><br>
<br>
However, if you are willing to choose two points yourself in ChimeraX, you can measure the distance between them. Some possible approaches:<br>
<br>
(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<br>
<br>
(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<br>
<br>
mouse right "tape measure"<br>
<br>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#mousemode">https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#mousemode</a>><br>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html#tapemeasure">https://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html#tapemeasure</a>><br>
<br>
...and then right click-drag to do the measurements.<br>
<br>
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.<br>
<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D. <br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
<br>
> On Jul 26, 2022, at 8:18 PM, SANTOSH RAMA BHADRA RAO TATA via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:<br>
> <br>
> Good day Meng,<br>
> <br>
> I'm trying to find the tutorial for the measuring the pore diameter. Can you please help me which protocol goes well with it.
<br>
> <br>
> Thanking you,<br>
> <br>
> With best wishes,<br>
> Tata Santosh Rama Bhadra Rao,<br>
> PhD Scholar,<br>
> C/O Prof Helen Irving,<br>
> La Trobe university,<br>
> Bendigo, Vic-3550,<br>
> Australia.<br>
> Email: 19807877@students.latrobe.edu.au; <br>
> S.Tata@latrobe.edu.au<br>
> Phone: 0499263974<br>
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