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Hi Tom,
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<div>Thank you so much for the prompt reply and a detailed solution!</div>
<div>I'll download the daily build and test the method.</div>
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<div>Best,</div>
Xin
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Tom Goddard <goddard@sonic.net><br>
<b>Sent:</b> Monday, June 6, 2022 7:35 PM<br>
<b>To:</b> Dai, Xin <xdai@bnl.gov><br>
<b>Cc:</b> chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [chimerax-users] Save the map after surface dust</font>
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<div class="" style="word-wrap:break-word; line-break:after-white-space">Hi Xin,
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<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>
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<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>open 11638 from emdb</div>
<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>volume #1 level 0.04</div>
<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>surface dust #1 size 2</div>
<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>volume mask #1 surface #1</div>
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<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>
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<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>open 11638 from emdb</div>
<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>volume #1 level 0.04</div>
<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>surface dust #1 size 2</div>
<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>surface invert #1</div>
<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>volume mask #1 surface #1 invert true</div>
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<div>This has the drawback that if you later show a lower threshold, new dust that has not been zeroed will appear.</div>
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<div><span class="x_Apple-tab-span" style="white-space:pre"></span>Tom</div>
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<div><img id="x_4C843F51-D2C3-4393-8F86-8D4F7A23F73A" width="446" height="413" class="" data-outlook-trace="F:1|T:1" src="cid:1555D4E3-9D44-4645-AC8D-B38B47CF5996"><br class="">
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<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>
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<span class="" style="background-color:transparent">Dear ChimeraX developers,</span></div>
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<span class="" style="background-color:transparent">I'm trying to save a density map following the command "surface dust".</span></div>
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<span class="" style="background-color:transparent">However, the map saved remains to be the original one. Is there any command to save the cleaned map?</span></div>
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<span class="" style="background-color:transparent">I found this old post </span><a target="_blank" href="https://urldefense.com/v3/__http://www.cgl.ucsf.edu/pipermail/chimera-dev/2015/001263.html__;!!P4SdNyxKAPE!ByBxI2Q_tuzI9qF8blIWl1sCxmNT-WCnFApXScb2ykdRXiMlAdCLCF59WUH5eisQqIZa__1kA5JP$" class="x_editor-rtfLink" style="color:rgb(74,110,224); background-color:transparent"><span class="" style="background-color:transparent">http://www.cgl.ucsf.edu/pipermail/chimera-dev/2015/001263.html</span></a><span class="" style="background-color:transparent"> asking
the same question using Chimera.</span></div>
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<span class="" style="background-color:transparent">But unfortunately, it's not working for me.</span></div>
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<span class="" style="background-color:transparent">Thank you,</span></div>
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<span class="" style="background-color:transparent">Xin</span></div>
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<span class="" style="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; text-decoration:none; float:none; display:inline!important">_______________________________________________</span><br class="" style="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; text-decoration:none">
<span class="" style="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; text-decoration:none; float:none; display:inline!important">ChimeraX-users
mailing list</span><br class="" style="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; text-decoration:none">
<a href="mailto:ChimeraX-users@cgl.ucsf.edu" class="" 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">ChimeraX-users@cgl.ucsf.edu</a><br class="" style="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; text-decoration:none">
<span class="" style="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; text-decoration:none; float:none; display:inline!important">Manage
subscription:</span><br class="" style="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; text-decoration:none">
<a href="https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users__;!!P4SdNyxKAPE!ByBxI2Q_tuzI9qF8blIWl1sCxmNT-WCnFApXScb2ykdRXiMlAdCLCF59WUH5eisQqIZa_6Kr7pUk$" class="" 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">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a></div>
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