<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 Bertrand,<div class=""><br class=""></div><div class=""> I'm not sure what you mean by "the surface cap is transparent". Maybe you mean there is no surface cap at all?</div><div class=""><br class=""></div><div class=""> In my tests the clip caps and coloring of caps all worked. The one tricky part is "surface dust #1" is going to hide small surface caps if you run that command after clipping because surface caps are a submodel #1.1.1 of the surface and your dust command applies to everything under model #1. You probably don't want surface dust to effect the caps so you could just run the "surface dust #1" command before you do the clipping, then it won't apply to the caps because the cap model did not exist when surface dust was run. It may be best if surface dust did not apply to caps, but that is not how it is working right now.</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><br class=""><blockquote type="cite" class=""><div class="">On Nov 6, 2019, at 10:34 AM, bertrand beckert <<a href="mailto:bertrand.beckert@gmail.com" class="">bertrand.beckert@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="">Hi All,</div><div class=""><br class=""></div><div class="">I have been recently trying to color a volume by a map value...</div><div class="">So far it worked really well using the color command....</div><div class=""><br class=""></div><div class="">color sample #1 map #2 offset 0.1 palette " values"<br class=""></div><div class=""><br class=""></div><div class="">But my problem is the following: when I clip the volume the surface cap is now transparent... is there a way to have the surface cap not transparent but instead colored according to the map value like it is in Chimera?<br class=""></div><div class=""><br class=""></div><div class="">Also another thing, I usually do is the following: <br class=""></div><div class=""><br class=""></div><div class="">open volume1.mrc</div><div class="">volume surfaceSmoothing true</div><div class="">surface dust #1</div><div class="">lighting soft</div><div class=""><br class=""></div><div class="">Then, when I clip through the map the surface cap is again transparent unless dust is turn off (suface undust #1)... I also tried surface cap false and then true but nothing changes... <span style="font-family: Times; font-size: inherit; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: 700; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; background-color: rgb(221, 221, 221); display: inline; float: none;" class=""></span></div><div class=""><br class=""></div><div class="">Is there a way around it? or does the surface dust function is somehow turn the surface cap always transparent? <br class=""></div><div class=""><br class=""></div><div class="">Thanks for the hard work and the nice software!</div><div class=""><br class=""></div><div class="">Best</div><div class=""><br class=""></div><div class="">Bertrand<br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><span class="gmail-gI"><span class=""></span></span></div></div>
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