<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Gary,<div class=""><br class=""></div><div class=""> 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</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>sop hideDust #0 size 25</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>sop invertShown #0</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>mask #0 #0 invert true</div><div class=""><br class=""></div><div class="">Would be nice to make this easier -- maybe in our next generation Chimera.</div><div class=""><br class=""></div><div class=""> Tom</div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Dec 8, 2015, at 6:35 PM, Tom Goddard wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html charset=us-ascii" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Gary,<div class=""><br class=""></div><div class=""> 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</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>mask #0 sel invert true</div><div class=""><br class=""></div><div class="">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.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div class=""><br class=""></div><div class=""></div></div><span id="cid:F7CA7D41-EC6A-4ADD-BEC5-EE2A42CEA0C4"><surfinvert.py></span><meta http-equiv="Content-Type" content="text/html charset=us-ascii" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class=""></div><div class=""><br class=""></div><div class="">The surfinvert.py script is also on the Chimera Python scripts page</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts" class="">http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts</a></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><div class=""><blockquote type="cite" class=""><div class="">On Dec 8, 2015, at 5:05 PM, Gang (Gary) Ren wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">Hi Tom,<br class=""><br class="">I like the density map after hide density map, is there any way to save the<br class="">density map after dust hide? Every time I save the density map, it saved the<br class="">original map instead of density map after hidden dust.<br class=""><br class="">Thanks a lot<br class="">Gary<br class=""><br class=""><br class=""><br class=""><br class=""></div></div></blockquote></div><br class=""></div></div></div></blockquote></div><br class=""></div></body></html>