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<p>Hi,<br>
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<p>Not sure if this is possible in ChimeraX yet but can do this in Chimera. Use map segmentation to separate green from grey. Then use surface measure tool (Mesure and color Blobs) to measure the surface area. <br>
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<p>Best wishes,<br>
Reza<br>
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Reza Khayat, PhD
<div>Associate Professor </div>
<div>City College of New York</div>
<div>Department of Chemistry and Biochemistry</div>
<div>New York, NY 10031</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of Y. Mutum <ym337@cam.ac.uk><br>
<b>Sent:</b> Tuesday, May 18, 2021 4:47 PM<br>
<b>To:</b> chimerax-users@cgl.ucsf.edu<br>
<b>Subject:</b> [EXTERNAL] [chimerax-users] Measuring surface area of a colored portion of the map</font>
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Hi</div>
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This problem relates to surface area of a low-resolution EM map using ChimeraX</div>
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<br>
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I have opened the following map and the corresponding model using the following commands in ChimeraX. </div>
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<span style="margin:0px; font-size:12pt">>>> open 4uq8; open 2676 from emdb</span><br>
<span style="margin:0px; font-size:12pt">>>> color #1 green; color zone #2 near #1 dist 4</span></div>
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As many parts of the map are unmodelled, I am interested 'how much of the map is unmodelled' in terms of surface area. This is mainly because the model is not accurate and I am trying to only use the raw-data (map) to estimate the surface area and avoid using
the model.</div>
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<br>
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Is there a way to figure out how much of the map is unmodelled in terms of surface area? In this case, count the number of '<b>outer pixels of a map</b>' that are colored green or gray, at a given map contour? </div>
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Could you please help with a way to measure this <b>without </b>using the 'volume splitbyzone' command?</div>
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Thanks</div>
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Yaikhomba</div>
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<img size="724538" tabindex="-1" style="max-width:100%" src="cid:71184965-9ba5-4374-82b3-bd2b264b4b0c"><br>
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