<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Xin,<div class=""><br class=""></div><div class=""> The old message you found was for Chimera. Here is how to save the map without the dust in ChimeraX. The simplest way is to set map values outside the displayed surface to zero.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>open 11638 from emdb</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>volume #1 level 0.04</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>surface dust #1 size 2</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>volume mask #1 surface #1</div><div class=""><br class=""></div><div class="">A drawback of that is that the map drops sharply to zero outside the shown contour level which can make it look jagged. Another approach is to zero the dust, which can be done by showing only the dust surface and zero everything inside that surface. This uses the "surface invert" command that I just added and will be in tomorrow's ChimeraX daily build (not in 1.4).</div><div class=""><br class=""></div><div class=""><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>open 11638 from emdb</div><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>volume #1 level 0.04</div><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>surface dust #1 size 2</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>surface invert #1</div><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>volume mask #1 surface #1 invert true</div></div><div class=""><br class=""><div>This has the drawback that if you later show a lower threshold, new dust that has not been zeroed will appear.</div><div><br class=""></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div><br class=""></div><div><img apple-inline="yes" id="4C843F51-D2C3-4393-8F86-8D4F7A23F73A" width="446" height="413" src="cid:1555D4E3-9D44-4645-AC8D-B38B47CF5996" class=""><br class=""><blockquote type="cite" class=""><div class="">On Jun 6, 2022, at 3:29 PM, Dai, Xin via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta charset="UTF-8" class=""><div style="margin-top: 0pt; margin-bottom: 0pt; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; color: rgb(14, 16, 26); background-color: transparent;" class=""><span data-preserver-spaces="true" style="background-color: transparent;" class="">Dear ChimeraX developers,</span></div><div style="margin-top: 0pt; margin-bottom: 0pt; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; color: rgb(14, 16, 26); background-color: transparent;" class=""><br class=""></div><div style="margin-top: 0pt; margin-bottom: 0pt; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; color: rgb(14, 16, 26); background-color: transparent;" class=""><span data-preserver-spaces="true" style="background-color: transparent;" class="">I'm trying to save a density map following the command "surface dust".</span></div><div style="margin-top: 0pt; margin-bottom: 0pt; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; color: rgb(14, 16, 26); background-color: transparent;" class=""><span data-preserver-spaces="true" style="background-color: transparent;" class="">However, the map saved remains to be the original one. Is there any command to save the cleaned map?</span></div><div style="margin-top: 0pt; margin-bottom: 0pt; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; color: rgb(14, 16, 26); background-color: transparent;" class=""><br class=""></div><div style="margin-top: 0pt; margin-bottom: 0pt; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; color: rgb(14, 16, 26); background-color: transparent;" class=""><span data-preserver-spaces="true" style="background-color: transparent;" class="">I found this old post </span><a target="_blank" href="http://www.cgl.ucsf.edu/pipermail/chimera-dev/2015/001263.html" class="editor-rtfLink" style="color: rgb(74, 110, 224); background-color: transparent;"><span data-preserver-spaces="true" style="background-color: transparent;" class="">http://www.cgl.ucsf.edu/pipermail/chimera-dev/2015/001263.html</span></a><span data-preserver-spaces="true" style="background-color: transparent;" class=""> asking the same question using Chimera.</span></div><div style="margin-top: 0pt; margin-bottom: 0pt; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; color: rgb(14, 16, 26); background-color: transparent;" class=""><span data-preserver-spaces="true" style="background-color: transparent;" class="">But unfortunately, it's not working for me.</span></div><div style="margin-top: 0pt; margin-bottom: 0pt; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; color: rgb(14, 16, 26); background-color: transparent;" class=""><br class=""></div><div style="margin-top: 0pt; margin-bottom: 0pt; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; color: rgb(14, 16, 26); background-color: transparent;" class=""><span data-preserver-spaces="true" style="background-color: transparent;" class="">Thank you,</span></div><div style="margin-top: 0pt; margin-bottom: 0pt; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; color: rgb(14, 16, 26); background-color: transparent;" class=""><span data-preserver-spaces="true" style="background-color: transparent;" class="">Xin</span></div><div style="margin-top: 0pt; margin-bottom: 0pt; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; color: rgb(14, 16, 26); background-color: transparent;" class=""><br class=""></div><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">ChimeraX-users mailing list</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><a href="mailto:ChimeraX-users@cgl.ucsf.edu" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">ChimeraX-users@cgl.ucsf.edu</a><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Manage subscription:</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a></div></blockquote></div><br class=""></div></body></html>