<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div class="">Hi Juleen,</div><div class=""><br class=""></div><div class=""> In our newer program ChimeraX there is the "mark connected" command that places a marker on each connected piece of a surface.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/marker.html" class="">https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/marker.html</a></div><div class=""><br class=""></div><div class="">I just added a "stats" option to output measurements for each blob including the surface area, enclosed volume, and number of holes. This will be tonight's ChimeraX builds.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://www.rbvi.ucsf.edu/chimerax/download.html#daily" class="">https://www.rbvi.ucsf.edu/chimerax/download.html#daily</a></div><div class=""><br class=""></div><div class="">The mark connected command originally from this ChimeraX example code</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://rbvi.github.io/chimerax-recipes/mark_blobs/mark_blobs.html" class="">https://rbvi.github.io/chimerax-recipes/mark_blobs/mark_blobs.html</a></div><div class=""><br class=""></div><div class=""> Tom</div><div class=""><br class=""></div><div class="">> open 22000 from emdb</div><div class="">> volume #1 level 0.6903</div><div class="">> surface dust #1 size 10</div><div class=""><br class=""></div><div class="">> marker connected #1 stats true</div><div class=""><br class=""></div><div class="">Found 21 connected surface pieces</div><div class="">Surface #1.1 has 21 visible blobs</div><div class=""># id, center xyz, surface area, enclosed volume, holes</div><div class=""> 1 154.58 152.55 149.36 108.7 43.23 0</div><div class=""> 2 173.32 149.15 156.33 212.8 86.06 0</div><div class=""> 3 156.96 165.48 158.25 320.1 148.3 0</div><div class=""> 4 160.32 175.48 154.98 98.6 38.59 0</div><div class=""> 5 143.37 151.62 162.12 77.07 25.17 0</div><div>...</div><div><br class=""></div><div><br class=""><blockquote type="cite" class=""><div class="">On Dec 14, 2020, at 7:58 AM, Juleen Dickson <<a href="mailto:jdickson6@gmail.com" class="">jdickson6@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Good Morning Everyone,<div class=""><br class=""></div><div class="">I fear the answer to my question is probably 'no' but I wanted to ask the experts first. I have segmentation of vesicles that I did from a cryo-EM tomogram that I did in EMAN2. I can open the segmentations and view them in chimera, however, I wanted to find a way to extract volume and surface area data on the segmentations so I can do statistics on them. If I use the Volume--> Measure and color blobs, the individual blob information will show up in the log. I am not sure if this information is accurate. Is there away to do this for all of the vesicles and download the data, maybe with the volume--> Segment map? If so, how do I do it? Thanks for your help.</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">Cheers,</div><div class="">Juleen</div><div class=""><br clear="all" class=""><div class=""><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><font face="Times New Roman" size="3" class="">
</font><div style="margin: 0in 0in 0pt; line-height: normal;" class=""><span style="font-family:"Times New Roman","serif";font-size:12pt" class="">"Never interrupt someone doing what
you said couldn't be done." </span></div><font face="Times New Roman" size="3" class="">
</font><div style="margin: 0in 0in 0pt; text-align: right; line-height: normal;" class=""><b class=""><span style="font-family:"Times New Roman","serif";font-size:12pt" class="">--Amelia
Earhart,<br class="">
American aviator</span></b></div><div style="margin: 0in 0in 0pt; text-align: left; line-height: normal;" class=""><span style="font-family:"Times New Roman","serif";font-size:12pt" class=""><br class=""></span></div><div style="margin: 0in 0in 0pt; text-align: left; line-height: normal;" class=""><span style="font-family:"Times New Roman","serif";font-size:12pt" class="">"Friends... they cherish one another's hopes. They are kind to one another's dreams." </span></div><div style="margin: 0in 0in 0pt; text-align: left; line-height: normal;" class=""><span style="font-family:"Times New Roman","serif";font-size:12pt" class=""><br class=""></span></div><div style="margin: 0in 0in 0pt; text-align: right; line-height: normal;" class=""><span style="font-family:"Times New Roman","serif";font-size:12pt" class=""><strong class="">-- Henry David Thoreau</strong></span></div><h1 style="margin:0px 0px 0.5em;padding:0px;border:0px;font-weight:200;font-stretch:inherit;font-size:36px;line-height:inherit;font-family:"Helvetica Neue",HelveticaNeue-Thin,"Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;color:rgb(77,77,77)" class=""><b style="color:rgb(31,73,125);font-family:Calibri,sans-serif;font-size:13.3333px" class=""><i class="">“Life isn’t about waiting for the storm to pass. It’s about learning how to dance in the rain…” -Vivian Greene</i></b><br class=""></h1><div style="margin: 0in 0in 0pt; text-align: right; line-height: normal;" class=""><span style="font-family:"Times New Roman","serif";font-size:12pt" class=""><strong class=""><br class=""></strong></span></div><font face="Times New Roman" size="3" class="">
</font></div></div></div></div></div></div></div>
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