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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Hi Tom,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Wow.. that will be awesome!! I can’t wait to use this new operation. The operation in Chimera is so cool, we love it.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Best regards<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Gary<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> Tom Goddard [mailto:goddard@sonic.net] <br><b>Sent:</b> Tuesday, December 08, 2015 6:53 PM<br><b>To:</b> chimera-dev@cgl.ucsf.edu<br><b>Cc:</b> Xiaobo Zhai; Gang (Gary) Ren<br><b>Subject:</b> Re: Save the map after hide dust<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Hi Gary,<o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal> I made it a bit easier to invert the shown portion of the map surface by adding an "sop invertShown" command. It will be in tonight's daily build. So to mask the dust on map #0 you could use<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal><span class=apple-tab-span> </span>sop hideDust #0 size 25<o:p></o:p></p></div><div><p class=MsoNormal><span class=apple-tab-span> </span>sop invertShown #0<o:p></o:p></p></div><div><p class=MsoNormal><span class=apple-tab-span> </span>mask #0 #0 invert true<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Would be nice to make this easier -- maybe in our next generation Chimera.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal> Tom<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p><div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><p class=MsoNormal>On Dec 8, 2015, at 6:35 PM, Tom Goddard wrote:<o:p></o:p></p></div><p class=MsoNormal><o:p> </o:p></p><div><div><p class=MsoNormal>Hi Gary,<o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal> Good to hear from you. The hide dust feature does not change the density map, it only hides the small connected surface pieces. You could set the map grid points to zero inside the dust blobs with the mask command. But first you need to be able to show only the dust and there is no command to do that. I've attached a Python script that does that. You select the map surface (ctrl-click) that you have done hide dust on, then open the surfinvert.py script to show only the dust. Then use the mask command<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal><span class=apple-tab-span> </span>mask #0 sel invert true<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>to mask the density map (#0) to the selected surface (dust blobs only shown) and invert, since you want to keep everything outside the dust blobs, not everything inside the dust blobs. I tried it, works. But if you lower the threshold on the new map then of course you see more dust.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal><span class=apple-tab-span> </span>Tom<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div></div><p class=MsoNormal><surfinvert.py><o:p></o:p></p><div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>The surfinvert.py script is also on the Chimera Python scripts page<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal><span class=apple-tab-span> </span><a href="http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts">http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts</a><o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p><div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><p class=MsoNormal>On Dec 8, 2015, at 5:05 PM, Gang (Gary) Ren wrote:<o:p></o:p></p></div><p class=MsoNormal><o:p> </o:p></p><div><div><p class=MsoNormal style='margin-bottom:12.0pt'>Hi Tom,<br><br>I like the density map after hide density map, is there any way to save the<br>density map after dust hide? Every time I save the density map, it saved the<br>original map instead of density map after hidden dust.<br><br>Thanks a lot<br>Gary<br><br><br><br><o:p></o:p></p></div></div></blockquote></div><p class=MsoNormal><o:p> </o:p></p></div></div></div></blockquote></div><p class=MsoNormal><o:p> </o:p></p></div></div></body></html>