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Hi Tom, Elaine and Reza</div>
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Thanks for the suggestions - I will try these and get back.</div>
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Thanks</div>
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Yaikhomba</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Tom Goddard <goddard@sonic.net><br>
<b>Sent:</b> 19 May 2021 02:32<br>
<b>To:</b> Y. Mutum <ym337@cam.ac.uk><br>
<b>Cc:</b> chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [chimerax-users] Measuring surface area of a colored portion of the map</font>
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<div class="" style="word-wrap:break-word; line-break:after-white-space">Hi Yaikhomba,
<div class=""> </div>
<div class=""> I added to ChimeraX a command "surface splitbycolor #3" to split a surface model into separate surfaces for each color of the original surface. Then you can use "measure area #4.1" to measure surface area of different colored pieces. The surfaces
in ChimeraX are made up of triangles, and colors are only assigned to the 3 vertices. Single color triangles (all 3 vertices have the same color) are put into separate surface models by color called "piece 1", "piece 2", .... And triangles that are multicolored
are put into a model called "multicolor". Usually single color patches are separated by a thin line of multicolor triangles that bridge the two single colored regions.</div>
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<div class=""> Thanks for sending me an explanation (private communication) of why you want to measure the surface area of colored patches. I don't fully understand it and I am not sure it will be useful, but you can try. Will be in tonight's ChimeraX daily
builds on the download web page.</div>
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<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>Tom</div>
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<div class="">Map surface at left split by color on right. Then I used drag mouse mode to move some of the colored pieces. Note the "multicolor" boundary line left where I moved away pieces.</div>
<div class=""><img id="x_9E87D810-AF99-4D15-B227-CCB04AAC97EE" width="676" height="292" class="" data-outlook-trace="F:1|T:1" src="cid:FB0DA37D-E31F-40B5-BB24-3E49C4972D01"><br class="">
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<blockquote type="cite" class="">
<div class="">On May 18, 2021, at 2:35 PM, Tom Goddard <<a href="mailto:goddard@sonic.net" class="">goddard@sonic.net</a>> wrote:</div>
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<div class="" style="word-wrap:break-word; line-break:after-white-space">Hi Yaikhomba,
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<div class=""> Why do you want surface area instead of volume? Volume seems more sensible as it would be very closely related to the number of modeled and unmodeled atoms. Also volume is easy to get using command "volume splitbyzone" and "measure volume".</div>
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<div class=""> If you have a good reason for wanting surface area it would not be very hard to do it with some Python code if you ignore the triangles of the surface that have a mix of green and gray vertex colors. I can provide that Python code if you give
a good reason why surface area is better than volume.</div>
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<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>Tom</div>
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<div class="">On May 18, 2021, at 1:47 PM, Y. Mutum <<a href="mailto:ym337@cam.ac.uk" class="">ym337@cam.ac.uk</a>> wrote:</div>
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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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I have opened the following map and the corresponding model using the following commands in ChimeraX. </div>
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<span class="" style="margin:0px; font-size:12pt">>>> open 4uq8; open 2676 from emdb</span><br class="">
<span class="" 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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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 class="">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 class="">without<span class="x_Apple-converted-space"> </span></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" class="" id="x_705D342E-22FF-4D6E-A2CD-7E1E84B4EB0A" style="max-width:100%" data-outlook-trace="F:2|T:2" src="cid:71184965-9ba5-4374-82b3-bd2b264b4b0c"><br class="">
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