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<div class="">Hello Heather,</div>
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Maybe measure distances between atoms chosen to get you as close as possible to the edges on the inside of the cavity, and then work out the volume geometrically? <a href="https://en.wikipedia.org/wiki/Regular_icosahedron#Area_and_volume" class="">https://en.wikipedia.org/wiki/Regular_icosahedron#Area_and_volume</a> (of
course, adjust according to the type of icosahedron you are dealing with, if it’s not a "regular" one).
<div class="">Seems like it would be a decent approximation.<br class="">
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<div class="">Measuring distances between atoms in ChimeraX can be done two ways:</div>
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<div class="">- interactively: <a href="https://www.cgl.ucsf.edu/chimerax/docs/user/tools/distances.html" class="">https://www.cgl.ucsf.edu/chimerax/docs/user/tools/distances.html</a></div>
<div class="">- or with a command, if you know which atoms to select (this can be figured out interactively by hovering the mouse pointer on the atoms): <a href="https://www.cgl.ucsf.edu/chimerax/docs/user/commands/distance.html" class="">https://www.cgl.ucsf.edu/chimerax/docs/user/commands/distance.html</a></div>
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<div class="">I hope this helps,<br class="">
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Guillaume</div>
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<blockquote type="cite" class="">
<div class="">On 3 Nov 2021, at 18:38, Noriega, Heather via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div>
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<div dir="auto" class="">What other ways can you measure the inter space of the icosahedral?<br class="">
<br class="">
<div data-smartmail="gmail_signature" class="">Thank you,<br class="">
<br class="">
Heather Noriega<br class="">
PhD-Pharmaceutical Science student<br class="">
College of Pharmacy<br class="">
Howard University<br class="">
<a href="mailto:heather.noriega@bison.howard.edu" class="">heather.noriega@bison.howard.edu</a>
<br class="">
520-203-1883</div>
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<div dir="ltr" class="gmail_attr">On Wed, Nov 3, 2021, 12:09 PM Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>> wrote:<br class="">
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<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Heather,<br class="">
I guess my first question is "why would you want to do that?" If the goal is to measure the cavity volume, there may be other ways. I'm not aware of any ChimeraX capability to fill it with waters (you may have to write your own code if that's what you really
want to do). <br class="">
<br class="">
In general you can count the waters (or any other residue type) in some structure using a similar method to what I described recently on the chimera-users list, except that to show the Selection Inspector you click the green magnifying glass on the top bar
icons of ChimeraX instead of the lower-right corner of the Chimera window.<br class="">
<<a href="https://plato.cgl.ucsf.edu/pipermail/chimera-users/2021-November/018182.html" rel="noreferrer noreferrer" target="_blank" class="">https://plato.cgl.ucsf.edu/pipermail/chimera-users/2021-November/018182.html</a>><br class="">
<br class="">
I hope this helps,<br class="">
ELaine<br class="">
-----<br class="">
Elaine C. Meng, Ph.D. <br class="">
UCSF Chimera(X) team<br class="">
Department of Pharmaceutical Chemistry<br class="">
University of California, San Francisco<br class="">
<br class="">
> On Nov 3, 2021, at 6:20 AM, Noriega, Heather via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank" rel="noreferrer" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:<br class="">
> <br class="">
> Good morning,<br class="">
> I am working on trying to find a measurement inside my alphafold prediction icosahedral. My advisor mentioned using the water molecules to fill the inside and then use a counter of some sort. I have no idea how to start this, I have been reading the volume
commands but am still having a hard time. Can you direct me to 1) fill only the inside of my icosahedral? and 2) how to count the water molecules inside?<br class="">
> Thank you,<br class="">
<br class="">
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