<div dir="ltr"><div>Dear Elaine</div><div><br></div><div>Thank you for replying.</div><div><br></div><div>I'm Matsui.</div><div><br></div><div>I apologize for my misunderstanding.</div><div><span style="font-family:inherit;font-style:inherit;font-variant-ligatures:inherit;font-variant-caps:inherit;color:rgb(45,47,61);font-size:18px;letter-spacing:0.3px"><br></span></div><div><span style="font-family:inherit;font-style:inherit;font-variant-ligatures:inherit;font-variant-caps:inherit;color:rgb(45,47,61);letter-spacing:0.3px">I understand.</span></div><div><div dir="ltr" data-smartmail="gmail_signature"><div dir="ltr"><div><span style="color:rgb(34,34,34)">------------------------------</span><span style="color:rgb(34,34,34)">------------------------------</span><span style="color:rgb(34,34,34)">---------------</span><br></div><div>Kenji Matsui<br></div><div><span style="color:rgb(34,34,34)"> Graduate School of Tokyo University of Agriculture and Technology M2</span><br style="color:rgb(34,34,34)"><span style="color:rgb(34,34,34)">2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan</span><br style="color:rgb(34,34,34)"><div style="color:rgb(34,34,34)"> Mail: <a href="mailto:s214903z@st.go.tuat.ac.jp" style="color:rgb(17,85,204)" target="_blank">s214903z@st.go.tuat.ac.jp</a></div></div></div></div></div><br><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">2022年9月8日(木) 0:58 Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" target="_blank">meng@cgl.ucsf.edu</a>>:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Dear Kenji,<br>
The example commands in my previous message are for ChimeraX, not Chimera.<br>
Elaine<br>
<br>
> On Sep 7, 2022, at 7:06 AM, Kenji MATSUI via Chimera-users <<a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank">chimera-users@cgl.ucsf.edu</a>> wrote:<br>
> <br>
> Dear Elane<br>
> <br>
> Thank you for your time and response.<br>
> <br>
> My name is Matsui, and I am a second-year master's student at a Japanese university.<br>
> <br>
> I am also using ChimeraX.<br>
> <br>
> But first I will try the method you showed me with chimera, and if it doesn't work, I will try it with chimeraX as well.<br>
> ---------------------------------------------------------------------------<br>
> Kenji Matsui<br>
> Graduate School of Tokyo University of Agriculture and Technology M2<br>
> 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan<br>
> Mail: <a href="mailto:s214903z@st.go.tuat.ac.jp" target="_blank">s214903z@st.go.tuat.ac.jp</a><br>
> <br>
> <br>
> 2022年9月6日(火) 23:30 Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" target="_blank">meng@cgl.ucsf.edu</a>>:<br>
> Hi Kenji,<br>
> You are using ChimeraX? I CC'd the ChimeraX address <a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank">chimerax-users@cgl.ucsf.edu</a> (different than <a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank">chimera-users@cgl.ucsf.edu</a>).<br>
> <br>
> The "measure buriedArea" command does not require picking any blobs. You just specify the parts that you want in the command line.<br>
> <<a href="https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea" rel="noreferrer" target="_blank">https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea</a>><br>
> <br>
> So, maybe something like command:<br>
> <br>
> measure buriedarea protein with ligand<br>
> <br>
> ...but maybe "ligand" doesn't get your ligand. You would have to use whatever kind of specification works for your ligand, e.g. if residue name is UNK, something like this instead:<br>
> <br>
> measure buriedarea protein with :UNK<br>
> <br>
> You sent a Pymol session... I don't use Pymol so I can't open that file, sorry.<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 Sep 5, 2022, at 9:45 PM, Kenji MATSUI via Chimera-users <<a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank">chimera-users@cgl.ucsf.edu</a>> wrote:<br>
> > <br>
> > Dear Chimera<br>
> > <br>
> > I am sorry to interrupt your busy schedule.<br>
> > <br>
> > My name is Matsui, and I am a second-year master's student at a Japanese university.<br>
> > Thank you for taking time out of your busy schedule to respond to my question the other day.<br>
> > <br>
> > We are investigating the buried surface area to see the magnitude of the interaction between protein and ligand.<br>
> > <br>
> > For this purpose, I calculated the solvent accessible area of the ligand. However, the value is 9955, which shows the entire surface area of the protein.<br>
> > <br>
> > What should I do? I am not in a hurry for answers , so I would appreciate a reply when you have the time.<br>
> > <br>
> > In this case, the ligand was in the binding pocket of the protein, so I would like to calculate the ligand's solvent contact area = buried surface area.<br>
> > <br>
> > I tried to check and tried , but it did not work.<br>
> > <br>
> > 1.See <a href="https://www.cgl.ucsf.edu/pipermail/chimera-users/2009-January/003521.html" rel="noreferrer" target="_blank">https://www.cgl.ucsf.edu/pipermail/chimera-users/2009-January/003521.html</a><br>
> > <br>
> > 2.Try to use measure blob using chimera X.<br>
> > Reference: <a href="https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea" rel="noreferrer" target="_blank">https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea</a><br>
> > <br>
> > However, I didn't know how to solve this command.<br>
> > Command ;ui mousemode right "pick blobs<br>
> > <br>
> > Reference; <a href="https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html" rel="noreferrer" target="_blank">https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html</a><br>
> > ---------------------------------------------------------------------------<br>
> > Kenji Matsui<br>
> > Graduate School of Tokyo University of Agriculture and Technology M2<br>
> > 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan<br>
> > <br>
> > <Buried_surface_area_LXRα_1UHL_24,25-epoxy_cholesterol (remove LXRβ_1P8D).pse>_______________________________________________<br>
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> <br>
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<br>
</blockquote></div></div>