<div dir="ltr">Dear Elaine C. Meng and
ChimeraX<div><br></div><div>I apologize for the mistake in sending the email to the wrong address.<br>Thank you for your quick response and polite reply. I will try it as soon as possible. I look forward to working with you again in the future.<br clear="all"><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><br></div><div><div>---------------------------------------------------------------------------<br></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></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">2021年12月18日(土) 4:20 Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu">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"><div style="overflow-wrap: break-word;"><div><br><blockquote type="cite"><div>Begin forwarded message:</div><br><div style="margin:0px"><span style="font-family:-webkit-system-font,"Helvetica Neue",Helvetica,sans-serif;color:rgb(0,0,0)"><b>From: </b></span><span style="font-family:-webkit-system-font,"Helvetica Neue",Helvetica,sans-serif">Kenji MATSUI <<a href="mailto:s214903z@st.go.tuat.ac.jp" target="_blank">s214903z@st.go.tuat.ac.jp</a>><br></span></div><div style="margin:0px"><span style="font-family:-webkit-system-font,"Helvetica Neue",Helvetica,sans-serif;color:rgb(0,0,0)"><b>Subject: </b></span><span style="font-family:-webkit-system-font,"Helvetica Neue",Helvetica,sans-serif"><b>Question: PDB file creation</b><br></span></div><div style="margin:0px"><span style="font-family:-webkit-system-font,"Helvetica Neue",Helvetica,sans-serif;color:rgb(0,0,0)"><b>Date: </b></span><span style="font-family:-webkit-system-font,"Helvetica Neue",Helvetica,sans-serif">December 16, 2021 at 7:20:41 PM PST</span></div><div style="margin:0px"><span style="font-family:-webkit-system-font,"Helvetica Neue",Helvetica,sans-serif;color:rgb(0,0,0)"><b>Cc: </b></span><span style="font-family:-webkit-system-font,"Helvetica Neue",Helvetica,sans-serif">Kaori Sakurai <<a href="mailto:sakuraik@cc.tuat.ac.jp" target="_blank">sakuraik@cc.tuat.ac.jp</a>><br></span></div><br><div><div dir="ltr"><div><div style="color:rgb(14,16,26);background-color:transparent;margin-top:0pt;margin-bottom:0pt"><span style="background:transparent;margin-top:0pt;margin-bottom:0pt">Dear UCSF ChimeraX</span></div><div style="color:rgb(14,16,26);background-color:transparent;margin-top:0pt;margin-bottom:0pt"><br></div><div style="color:rgb(14,16,26);background-color:transparent;margin-top:0pt;margin-bottom:0pt"><span style="background:transparent;margin-top:0pt;margin-bottom:0pt">Thank you for allowing me to use your software. I am Japanese, so I hope you will understand that there are some inappropriate expressions. I would like to ask you two questions.</span></div><div style="color:rgb(14,16,26);background-color:transparent;margin-top:0pt;margin-bottom:0pt"><br></div><div style="color:rgb(14,16,26);background-color:transparent;margin-top:0pt;margin-bottom:0pt"><span style="background:transparent;margin-top:0pt;margin-bottom:0pt">First, I would like to know how to convert a cxs file saved in Chimera X to a PDB file.</span></div><div style="color:rgb(14,16,26);background-color:transparent;margin-top:0pt;margin-bottom:0pt"><br></div><div style="color:rgb(14,16,26);background-color:transparent;margin-top:0pt;margin-bottom:0pt"><span style="background:transparent;margin-top:0pt;margin-bottom:0pt">Aim</span></div><div style="color:rgb(14,16,26);background-color:transparent;margin-top:0pt;margin-bottom:0pt"><span style="background:transparent;margin-top:0pt;margin-bottom:0pt">To display the interaction between a protein (osh4) and a ligand (OSW-1) in pymol</span></div><div style="color:rgb(14,16,26);background-color:transparent;margin-top:0pt;margin-bottom:0pt"><br></div><div style="color:rgb(14,16,26);background-color:transparent;margin-top:0pt;margin-bottom:0pt"><span style="background:transparent;margin-top:0pt;margin-bottom:0pt">Methods I have tried</span></div><div style="color:rgb(14,16,26);background-color:transparent;margin-top:0pt;margin-bottom:0pt"><span style="background:transparent;margin-top:0pt;margin-bottom:0pt">I found a way to convert mmCIF to PDB</span><span style="background-color:transparent"> file, but I could not find a site to convert cxs file to PDB file.</span></div><div style="color:rgb(14,16,26);background-color:transparent;margin-top:0pt;margin-bottom:0pt"><br></div><div style="color:rgb(14,16,26);background-color:transparent;margin-top:0pt;margin-bottom:0pt"><span style="background:transparent;margin-top:0pt;margin-bottom:0pt">Second, How to deal with the following error that appears when the structure of the osh4-OSW-1 complex is shown.</span></div><div style="color:rgb(14,16,26);background-color:transparent;margin-top:0pt;margin-bottom:0pt"><br></div><div style="color:rgb(14,16,26);background-color:transparent;margin-top:0pt;margin-bottom:0pt"><span style="background:transparent;margin-top:0pt;margin-bottom:0pt">APBS electron</span></div><div style="color:rgb(14,16,26);background-color:transparent;margin-top:0pt;margin-bottom:0pt"><span style="background:transparent;margin-top:0pt;margin-bottom:0pt">Error: The following residues are missing heavy (non-hydrogen) atoms, which may result in inaccurate electron density.</span></div><h1 style="color:rgb(14,16,26);background:transparent;margin-top:0pt;margin-bottom:0pt;font-weight:normal"><span style="background:transparent;margin-top:0pt;margin-bottom:0pt"><font size="2">Thank you for your cooperation.</font></span></h1></div><div><p class="MsoNormal" style="margin:0mm;text-align:justify;font-size:10.5pt;font-family:游明朝,serif"></p></div><div><div dir="ltr"><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>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></div></div></div></div></blockquote><br></div><div>Hi Kenji,<div>I omitted your cxs file from this message since I thought maybe you wanted to keep it private (messages on this <a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank">chimerax-users@cgl.ucsf.edu</a> mailing list can be seen by the public).</div><div><br></div><div>I didn't see that APBS error when I opened the cxs file in ChimeraX. It appears to be a message from another program (not ChimeraX): the APBS program, which calculates electrostatic potential. The error is exactly what it says: some residues in the structure are missing some atoms, which would affect the calculation of electrostatic potential values.</div><div><br></div><div>Short answer #1 is why not look at the interactions in ChimeraX instead of Pymol? You can calculate H-bonds, find contacts, etc. See this tutorial, for example</div><div><<a href="https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html" target="_blank">https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html</a>></div><div><br></div><div>Short answer #2 is that you can open the session (cxs) file in ChimeraX and then save a PDB file with the "save" command or the menu: File... Save... (choose Files of type: PDB). </div><div><br></div><div>HOWEVER, a longer answer may be required here because I can see from opening your cxs file that it contains many models, I guess a receptor (model #1) and ligands from docking (models #2-258) with only some ligands displayed (models #10-17). </div><div><br></div><div>I'm guessing you want to save only the ones that are displayed. You could save models #1,10-17 into one multi-model PDB, file but probably for analysis in Pymol or other programs, you would instead need to combine each ligand with receptor and save it separately. In other words, you may need to make a new model by combining #1 with #10, and then save the new single model to a PDB file. For example:</div><div><br></div><div>combine #1,10 modelId #300</div><div>save /Users/meng/Desktop/result10.pdb models #300 relModel #1 </div><div><br></div><div>Then repeat for other ligands, combining #1 with #11 to make a new model and saving that new model, combining #1 with #12, etc. See the help links below for the options of each command.</div><div><br></div><div>Save command:</div><div><<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb" target="_blank">https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb</a>></div><div>Combine command:</div><div><<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html" target="_blank">https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html</a>></div><div><br></div><div>I hope this helps,</div><div>Elaine<br><div><span style="border-collapse:separate;font-variant-ligatures:normal;font-variant-east-asian:normal;line-height:normal;border-spacing:0px"><div style="overflow-wrap: break-word;"><div>-----</div><div>Elaine C. Meng, Ph.D. </div><div>UCSF Chimera(X) team</div><div>Department of Pharmaceutical Chemistry</div><div>University of California, San Francisco</div><div><br></div></div></span></div></div></div><br></div></blockquote></div>