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Thanks Elaine. </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> Tuesday, December 29, 2020 5:17:14 PM<br>
<b>To:</b> Y. Mutum <ym337@cam.ac.uk><br>
<b>Cc:</b> chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [chimerax-users] Computing protein cavities</font>
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<div class="PlainText">Hi Yaikhomba,<br>
I'm not aware of any ChimeraX tools or plugins that will calculate the cavity volume directly. I assume you looked in the ChimeraX Toolshed yourself (what you get when you choose "more tools" from the menu) because any developers can upload their plugins and
we in the team here might not know much about them.<br>
<br>
You probably just need to search the web to try to find something.<br>
<br>
I can list a few web servers or programs, but I have no idea about reliability on large structures, so I would not call it a recommendation.<br>
<br>
Castp server calculates pocket volumes and areas<br>
<<a href="http://sts.bioe.uic.edu/castp/calculation.html">http://sts.bioe.uic.edu/castp/calculation.html</a>><br>
<br>
Some others may create a file that can be viewed in Chimera or ChimeraX as a surface blob, and then you could use Chimera or ChimeraX "measure volume" (or ChimeraX "measure blob") on that surface<br>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/measurements.html">https://rbvi.ucsf.edu/chimerax/docs/user/measurements.html</a>><br>
<br>
I list a couple of these below. However, their websites mainly mention "channels" so I don't know if they work well for all kinds of pockets.<br>
<br>
Voss Volume Voxelator<br>
<<a href="http://3vee.molmovdb.org/">http://3vee.molmovdb.org/</a>><br>
<br>
Moleonline <br>
<<a href="https://mole.upol.cz/">https://mole.upol.cz/</a>><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>
> On Dec 29, 2020, at 5:37 AM, Y. Mutum <ym337@cam.ac.uk> wrote:<br>
> <br>
> Hi<br>
> <br>
> This question is on calculating empty cavities of large protein complexes (~2 MDa) For example, the pdb-id: 6J5K. I have tried a few webservers and they are ignoring to calculate such large protein-pdb files as a whole.<br>
> <br>
> Does ChimeraX have tools that can be installed from the 'More-Tools' or an inbuilt one to calculate protein cavities in ChimeraX?
<br>
> If you could suggest external programs for computing cavities, that are reliable for such large protein-inputs, it would be also of a great help. The cavities need not be sealed by proteins all around - they can still be open to the bulk solvent.<br>
> <br>
> Thanks<br>
> Yaikhomba<br>
<br>
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