Save the map after surface dust
Dear ChimeraX developers, I'm trying to save a density map following the command "surface dust". However, the map saved remains to be the original one. Is there any command to save the cleaned map? I found this old post http://www.cgl.ucsf.edu/pipermail/chimera-dev/2015/001263.html asking the same question using Chimera. But unfortunately, it's not working for me. Thank you, Xin
Hi Xin, 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. open 11638 from emdb volume #1 level 0.04 surface dust #1 size 2 volume mask #1 surface #1 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). open 11638 from emdb volume #1 level 0.04 surface dust #1 size 2 surface invert #1 volume mask #1 surface #1 invert true This has the drawback that if you later show a lower threshold, new dust that has not been zeroed will appear. Tom
On Jun 6, 2022, at 3:29 PM, Dai, Xin via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX developers,
I'm trying to save a density map following the command "surface dust". However, the map saved remains to be the original one. Is there any command to save the cleaned map?
I found this old post http://www.cgl.ucsf.edu/pipermail/chimera-dev/2015/001263.html <http://www.cgl.ucsf.edu/pipermail/chimera-dev/2015/001263.html> asking the same question using Chimera. But unfortunately, it's not working for me.
Thank you, Xin
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Hi Tom, Thank you so much for the prompt reply and a detailed solution! I'll download the daily build and test the method. Best, Xin ________________________________ From: Tom Goddard <goddard@sonic.net> Sent: Monday, June 6, 2022 7:35 PM To: Dai, Xin <xdai@bnl.gov> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Save the map after surface dust Hi Xin, 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. open 11638 from emdb volume #1 level 0.04 surface dust #1 size 2 volume mask #1 surface #1 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). open 11638 from emdb volume #1 level 0.04 surface dust #1 size 2 surface invert #1 volume mask #1 surface #1 invert true This has the drawback that if you later show a lower threshold, new dust that has not been zeroed will appear. Tom [cid:1555D4E3-9D44-4645-AC8D-B38B47CF5996] On Jun 6, 2022, at 3:29 PM, Dai, Xin via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Dear ChimeraX developers, I'm trying to save a density map following the command "surface dust". However, the map saved remains to be the original one. Is there any command to save the cleaned map? I found this old post http://www.cgl.ucsf.edu/pipermail/chimera-dev/2015/001263.html<https://urldefense.com/v3/__http://www.cgl.ucsf.edu/pipermail/chimera-dev/2015/001263.html__;!!P4SdNyxKAPE!ByBxI2Q_tuzI9qF8blIWl1sCxmNT-WCnFApXScb2ykdRXiMlAdCLCF59WUH5eisQqIZa__1kA5JP$> asking the same question using Chimera. But unfortunately, it's not working for me. Thank you, Xin _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users<https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users__;!!P4SdNyxKAPE!ByBxI2Q_tuzI9qF8blIWl1sCxmNT-WCnFApXScb2ykdRXiMlAdCLCF59WUH5eisQqIZa_6Kr7pUk$>
participants (2)
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Dai, Xin -
Tom Goddard