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The figure you shared looks more like the cryoEM map than a surface generated from a pdb file.
<div class="">Why not download a map from EMDB? </div>
<div class="">There are several AAV maps, I made the attached image using EMD6470.</div>
<div class="">Looks even better in ChimeraX!</div>
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<div><span style="font-style: normal;" class="">David Bhella</span></div>
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<span style="font-size: 11px;" class="">Professor of Structural Virology</span></span><span style="font-size: 11px;" class=""><br class="">
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<div><span style="font-style: normal; font-size: 11px;" class="">Associate Director - MRC-University of Glasgow Centre for Virus Research</span></div>
<div><span style="font-style: normal; font-size: 11px;" class="">Director - Scottish Centre for Macromolecular Imaging</span></div>
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Sir Michael Stoker Building<br class="">
Garscube Campus<br class="">
464 Bearsden Road<br class="">
Glasgow G61 1QH<br class="">
Scotland (UK)<br class="">
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Telephone: 0141-330-3685<br class="">
Skype: d.bhella</span><br class="">
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<blockquote type="cite" class="">
<div class="">On 20 Sep 2019, at 23:29, Gampe, Robert <<a href="mailto:Robert.Gampe@pfizer.com" class="">Robert.Gampe@pfizer.com</a>> wrote:</div>
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<span style="font-size: 12pt;" class="">Hi Chimera Users<o:p class=""></o:p></span></div>
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<span style="font-size: 12pt;" class=""><o:p class=""> </o:p></span></div>
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<span style="font-size: 12pt;" class="">I need to calculate a radial distance plot from a surface representation of an Adeno Associated Virus structure as shown from literature below.<o:p class=""></o:p></span></div>
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<span style="font-size: 12pt;" class=""><o:p class=""> </o:p></span></div>
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<span style="font-size: 12pt;" class="">However the:<o:p class=""></o:p></span></div>
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<span style="font-size: 12pt;" class="">Action, Surface, Show<o:p class=""></o:p></span></li></ol>
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<span style="font-size: 12pt;" class="">command fails, reporting CHIMERA often fails for large structures ( AAV is easily over 200K atoms ) with multiple chain IDs ( I have 60 individual chain IDs for each of the 60 capsid proteins ).<o:p class=""></o:p></span></div>
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<span style="font-size: 12pt;" class=""><o:p class=""> </o:p></span></div>
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<span style="font-size: 12pt;" class="">Other CHIMERA popup suggestions did not resolve the problem either ( changing molecular surface parameters in the Inspect Selection ( actually didn’t see anything to change ) or in PREFERENCES - NEW SURFACES. I tried
using CHIMERA, Structure editing, change chain IDs to all chain A, but that was disallowed.<o:p class=""></o:p></span></div>
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<span style="font-size: 12pt;" class=""><o:p class=""> </o:p></span></div>
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<span style="font-size: 12pt;" class="">Summary: could not figure out how to get CHIMERA to calculate and display a surface representation of an AAV virus and then use that display to calculate radial coloring as shown below.<o:p class=""></o:p></span></div>
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<span style="font-size: 12pt;" class=""><o:p class=""> </o:p></span></div>
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<span style="font-size: 12pt;" class="">Any solutions greatly appreciated and thanks.<o:p class=""></o:p></span></div>
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<span style="font-size: 12pt;" class=""><o:p class=""> </o:p></span></div>
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<span style="font-size: 12pt;" class="">Rob<o:p class=""></o:p></span></div>
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<span style="font-size: 12pt;" class=""><o:p class=""> </o:p></span></div>
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<span style="font-size: 12pt;" class=""><o:p class=""> </o:p></span></div>
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<span style="font-size: 12pt;" class=""><o:p class=""> </o:p></span></div>
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<span style="font-size: 12pt;" class=""><span id="cid:image003.jpg@01D56FE1.62351B70"><image003.jpg></span></span><span class="Apple-converted-space"> </span><span id="cid:image004.jpg@01D56FE1.62351B70"><image004.jpg></span><span style="font-size: 12pt;" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 12pt;" class=""><o:p class=""> </o:p></span></div>
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<span style="font-size: 12pt;" class=""><o:p class=""> </o:p></span></div>
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</span><span style="font-size: 10pt; background-color: white;" class="">_________________________</span><span style="font-size: 10pt;" class=""><br class="">
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Robert Gampe, MS | Senior Scientist | RDRU Structural Biology| Pfizer Inc. <span class="Apple-converted-space"> </span><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt;" class="">7030 Kit Creek Rd, Morrisville, NC 27560<o:p class=""></o:p></span></div>
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<span style="font-size: 10pt;" class="">Office: 919-666-5969|</span><span style="font-size: 10pt; color: gray;" class=""><span class="Apple-converted-space"> </span></span><u class=""><span style="font-size: 10pt; color: blue;" class=""><a href="mailto:Robert.Gampe@pfizer.com" style="color: purple; text-decoration: underline;" class=""><span style="color: blue;" class="">Robert.Gampe@pfizer.com</span></a><o:p class=""></o:p></span></u></div>
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<span id="cid:image005.jpg@01D56FE1.62351B70"><image005.jpg></span><span style="font-size: 10pt; color: rgb(31, 73, 125);" class=""> <o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; background-color: white;" class="">_________________________</span><span style="font-size: 10pt;" class=""><o:p class=""></o:p></span></div>
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<o:p class=""> </o:p></div>
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