<div dir="ltr"><div>Dear Elaine</div><div><br></div><div>Thank you for your quick reply.<br></div><div><br></div>However, my only guess is that in ChimeraX, you did not correctly combine the receptor and ligand models into one model before saving it as a PDB file, or that when you saved you didn't save the combined model but some other model.<div>>Thank you for telling me exactly what the problem is.<br><div><br></div><div>In ChimeraX you have to use the "combine" command to make a new model, and then save the new model. There is no GUI for combining yet. After combining, then you can use either the "save" command or menu: File... Save to save the new model.<br>>Thank you for showing me exactly how to do it. I will do it as soon as possible.<br><div><br></div><div>Thanks to your help, I will be able to make progress in my research.</div><div><br></div><div> Thank you from the bottom of my heart.<br clear="all"><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>松井 健治<div> 東京農工大学大学院 工学府産業技術専攻 修士 </div><div>〒184-8588 東京都小金井市中町2-24-16</div><div> Mail: <a href="mailto:s214903z@st.go.tuat.ac.jp" target="_blank">s214903z@st.go.tuat.ac.jp</a><br></div><div><br></div></div></div></div><div>Kenji Matsui<br> Graduate School of Tokyo University of Agriculture and Technology<br>2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan<br><div> Mail: <a href="mailto:s214903z@st.go.tuat.ac.jp" target="_blank">s214903z@st.go.tuat.ac.jp</a></div></div><br><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">2021年12月21日(火) 3:24 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">In ChimeraX you have to use the "combine" command to make a new model, and then save the new model. There is no GUI for combining yet. After combining, then you can use either the "save" command or menu: File... Save to save the new model.<br>
<br>
My example used commands for both steps:<br>
<<a href="https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-December/003032.html" rel="noreferrer" target="_blank">https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-December/003032.html</a>><br>
<br>
Elaine<br>
<br>
<br>
> On Dec 20, 2021, at 9:46 AM, Elaine Meng via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank">chimerax-users@cgl.ucsf.edu</a>> wrote:<br>
> <br>
> Hi Kenji,<br>
> I don't really know how to use Pymol very well, so I can't help with that program. <br>
> <br>
> However, my only guess is that in ChimeraX, you did not correctly combine the receptor and ligand models into one model before saving it as a PDB file, or that when you saved you didn't save the combined model but some other model.<br>
> <br>
> I happened to have an extremely old version of Pymol on my old computer (it does not run on my current computer), and when I opened result10.pdb saved from your session with exactly the commands I sent you earlier, I could see that the ligand was displayed, see screenshot:<br>
> <br>
> <Screen Shot 2021-12-20 at 9.32.17 AM.png><br>
> <br>
> The reply I sent before with the exact commands that I used to make the file is here:<br>
> <<a href="https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-December/003032.html" rel="noreferrer" target="_blank">https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-December/003032.html</a>><br>
> <br>
> ...and I also attach that file, result10.pdb: <result10.pdb><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 Dec 19, 2021, at 10:14 PM, Kenji MATSUI via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank">chimerax-users@cgl.ucsf.edu</a>> wrote:<br>
>> <br>
>> Dear ChimeraX<br>
>> <br>
>> Thank you very much for your kind words in the past. When I opened the PDB file and mol2 file saved by pymol using the method you gave me, the ligands disappeared.<br>
>> <br>
>> How can I get pymol to display the ligands as well? <br>
>> <br>
>> Here is in detail.<br>
>> <br>
>> As you suggested, I created a new model by combining #1 and #10, and saved the newly single model in a PDB file. However, when I displayed this file in pymol, I could not see the ligand as shown in the figure.<br>
>> <image.png><br>
>> <image.png><br>
>> So we tried to align the ligand OSW-1 to the protein osh4 in this figure, but it was difficult to analyze because OSW-1 was far away from the distance of the protein osh4 as shown in the figure below.<br>
>> <br>
>> <image.png><br>
>> <br>
>> <br>
>> Refernece：Save command:<br>
>> <<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb" rel="noreferrer" target="_blank">https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb</a>><br>
>> <br>
>> Also, I've looked at tutorials and other sites on the Internet to try to figure out what's causing this, but no luck!<br>
>> <br>
>> I'm sorry for the many questions.<br>
>> ---------------------------------------------------------------------------<br>
>> Kenji Matsui<br>
>> Graduate School of Tokyo University of Agriculture and Technology<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>
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</blockquote></div></div></div></div></div>