<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=utf-8"><meta name=Generator content="Microsoft Word 15 (filtered medium)"><style><!--
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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>Yes, you understood correctly – I have a 3D map where I want to separate the detergent from the protein density by colour.<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 thought somehow the threshold density value should be somehow involved in that – because at a certain threshold I see no detergent...<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>But I will try all your proposed options.<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!<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<o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986">Mail</a> for Windows</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>Monday, July 18, 2022 10:32 PM<br><b>To: </b><a href="mailto:semchonok@gmail.com">Dmitry A. Semchonok</a><br><b>Cc: </b><a href="mailto:chimerax-users@cgl.ucsf.edu">chimerax-users@cgl.ucsf.edu</a><br><b>Subject: </b>Re: [chimerax-users] showing detergent around the protein</p></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Hi Dmitry,</p><p class=MsoNormal>Not sure I understand... it is all in the same map, I'm guessing, with density from both the detergent and the molecule(s) of interest. If there are some atoms by which you can define a distance zone (e.g. a fitted atomic structure or markers that you placed by hand), then you can try using Color Zone. </p><p class=MsoNormal><https://rbvi.ucsf.edu/chimerax/docs/user/tools/colorzone.html></p><p class=MsoNormal><https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone></p><p class=MsoNormal><https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#splitbyzone></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Or you could try to erase the detergent part by hand with Map Eraser (there would still be an additional copy of the full map for displaying the region that contains detergent):</p><p class=MsoNormal><https://rbvi.ucsf.edu/chimerax/docs/user/tools/maperaser.html></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Otherwise my only other idea is to run segmentation in hopes it would separate the detergent from the rest, but I don't know if that would work.</p><p class=MsoNormal><https://rbvi.ucsf.edu/chimerax/docs/user/tools/segment.html></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 Jul 18, 2022, at 1:16 PM, Dmitry A. 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>> Do you know how to colour the map in one colour and detergent in another?</p><p class=MsoNormal>> I work with membrane proteins and I would like to discriminate between density and detergent.</p><p class=MsoNormal>> </p><p class=MsoNormal>> Thank you!</p><p class=MsoNormal>> </p><p class=MsoNormal>> Kind regards,</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p></div></body></html>