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--></style></head><body lang=EN-US link=blue vlink="#954F72" style='word-wrap:break-word'><div class=WordSection1><p class=MsoNormal><span lang=EN-GB>Dear Elaine,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-GB>Thank you very much for the variety of solutions.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB>I believe you solved my issue! <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-GB>I am sure that (1) will work best for my project!<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-GB>Thanks again.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-GB>Kind regards,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB>Dmitry</span></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><div style='mso-element:para-border-div;border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal style='border:none;padding:0in'><b>From: </b><a href="mailto:meng@cgl.ucsf.edu">Elaine Meng</a><br><b>Sent: </b>Wednesday, November 9, 2022 7:05 PM<br><b>To: </b><a href="mailto:semchonok@gmail.com">Dmitry Semchonok</a><br><b>Cc: </b><a href="mailto:ChimeraX-users@cgl.ucsf.edu">ChimeraX Users Help</a><br><b>Subject: </b>Re: [chimerax-users] Density extraction</p></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Hi Dmitry,</p><p class=MsoNormal>I don't know how you plan to figure out which part is for one subunit if you don't have a structure. Some vague ideas are:</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>(1) segmentation, e.g. see "Segment Map"</p><p class=MsoNormal><https://www.rbvi.ucsf.edu/chimerax/docs/index.html></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>(2) if you can picture the part that you want, manual erasing, e.g. see "Map Eraser"</p><p class=MsoNormal><https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/maperaser.html></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>(3) create a surface that includes the part you want, e.g. some geometric shape with the "shape" command, and then use that surface in "volume mask"</p><p class=MsoNormal><https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#mask></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>You could also try fitting a homologous structure (if any is available), or get an AlphaFold prediction for your structure and fit that, then limit the density to what is surrounding the structure.</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>I hope this helps,</p><p class=MsoNormal>Elaine</p><p class=MsoNormal>-----</p><p class=MsoNormal>Elaine C. Meng, Ph.D. </p><p class=MsoNormal>UCSF Chimera(X) team</p><p class=MsoNormal>Department of Pharmaceutical Chemistry</p><p class=MsoNormal>University of California, San Francisco</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>> On Nov 9, 2022, at 1:15 AM, Dmitry Semchonok via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:</p><p class=MsoNormal>> </p><p class=MsoNormal>> Dear colleagues,</p><p class=MsoNormal>> </p><p class=MsoNormal>> I have a 3D map of the helix. </p><p class=MsoNormal>> </p><p class=MsoNormal>> 1. Do you know how can I extract 1 subunit? </p><p class=MsoNormal>> </p><p class=MsoNormal>> 2. Also, if there is no x-ray structure available.</p><p class=MsoNormal>> </p><p class=MsoNormal>> </p><p class=MsoNormal>> Thanks in advance.</p><p class=MsoNormal>> </p><p class=MsoNormal>> Kind regards,</p><p class=MsoNormal>> Dmitry</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p></div></body></html>