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Thanks a lot Elaine and Tom for your help!<br>
Have a nice we,<br>
Roberto<br>
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Inviato dal mio dispositivo Huawei<br>
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-------- Messaggio originale --------<br>
Oggetto: Re: [Chimera-users] Area central hole oligomer<br>
Da: Tom Goddard <br>
A: UCSF Chimera Mailing List <br>
CC: Roberto Marotta <br>
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<div dir="ltr">Another way to measure hole crosssectional area would be to multiply the map by -1 (vop scale #0 factor 1) so surfaces now surround low density instead of high density, then show just one plane cutting through the hole using Volume Viewer menu
Features / Region Bounds, then use the Measure and Color Blobs tool to click on the hole surface and report its area. Note the value reported is twice the hole area since the single plane surface is really 2 planar surfaces facing in opposite directions.</div>
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<div dir="ltr"> Tom</div>
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On Apr 13, 2019, at 8:30 AM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>> wrote:<br>
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<div dir="ltr">Hi Roberto,
<div class="">There isn’t a tool to do it in a single step, but you could try using Volume Tracer to add several markers around the hole when viewing your data as a plane, and then create a polygonal surface from those markers, then measure the area of that
surface. See "Markers: Creation" and "Surface Creation” in the Volume Tracer documentation:</div>
<div class=""><<a href="http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/framevolpath.html" class="">http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/framevolpath.html</a>></div>
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<div class="">Example shown in attached picture:</div>
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<div class="">I opened EMDB 1024 and showed a single plane as surfaces in Volume Viewer (you can use its menu: Feature…Planes). I started Volume Tracer from the Tools menu. In Volume Tracer: in Mouse menu I chose to place markers on data planes and link new
marker and then added several markers. Then to add link between first and last markers, in Mouse menu I chose to link consecutively selected markers and chose those two. (If you mess up you can select a marker and use the Actions menu in Volume Tracer to
delete it.) Now I had a closed loop of linked markers. Then in Volume Tracer, Features menu I chose Surface and then clicked the surface “Create” button (after clearing selection so that no markers were selected). Then in Model Panel you can see surface
is #2, so I used command “measure area #2” which reports surface are in the status line and Reply Log.</div>
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<div class="">There was a hole but you can’t see it in the picture because the yellow surface is covering it.</div>
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<div class="">This workflow is for an X, Y, or Z plane. If the hole axis is not aligned with data axes, then instead of using this planes approach you might have to show the full box but then use per-model clipping to slice at an angle. I did not try that.</div>
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<div class="">I hope this helps,</div>
<div class="">Elaine<br class="">
<div class="">
<div class="">-----<br class="">
Elaine C. Meng, Ph.D. <br class="">
UCSF Chimera(X) team<br class="">
Department of Pharmaceutical Chemistry<br class="">
University of California, San Francisco<br class="">
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<div class=""><Screen Shot 2019-04-13 at 8.18.24 AM.png></div>
<br class="">
<blockquote type="cite" class="">On Apr 12, 2019, at 11:34 PM, Roberto Marotta <<a href="mailto:Roberto.Marotta@iit.it" class="">Roberto.Marotta@iit.it</a>> wrote:<br class="">
<br class="">
Hi,<br class="">
I have the density map of a large oligomer resolved at 5 A. I would like to measure the area of the hole at the center of the oligomer. The five subunits that form the oligomer delimit the hole that is open and irregular in shape.<br class="">
My idea is to measure the area of the hole in a central slice of the map.<br class="">
<br class="">
Amy suggestions are really appreciated!<br class="">
Thank you,<br class="">
Roberto<br class="">
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