<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class="">A number of web sources say the program netfabb can “repair" surface meshes.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-May/008826.html" class="">http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-May/008826.html</a></div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://thingiverse-production-new.s3.amazonaws.com/assets/35/64/72/a2/77/Eduardos_Guide_for_3D_Printing_Proteins.pdf" class="">https://thingiverse-production-new.s3.amazonaws.com/assets/35/64/72/a2/77/Eduardos_Guide_for_3D_Printing_Proteins.pdf</a></div><div class=""><br class=""></div><div class=""> Tom</div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On May 9, 2016, at 12:32 AM, Jakob Suckale <<a href="mailto:jakob.suckale@uni-tuebingen.de" class="">jakob.suckale@uni-tuebingen.de</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="">Dear all,</div><div class=""><br class=""></div>A follow up on Tom's suggestion. I have tested MeshLab. It does indeed have functions that can be used to reduce internal surfaces (<a href="https://www.youtube.com/watch?v=9EHJQd3SREE" class="">https://www.youtube.com/watch?v=9EHJQd3SREE</a>) but it's far from a good solution. It is based on assigning a value to vertices based on visibility (Ambient Occlusion) and then removing the ones that have low scores. In a ribbon model, however, it often opens holes for example on the inside of a helix and it leaves many internal structures untouched.<div class=""><br class=""></div><div class="">All the best,<br class=""><br class="">Jakob</div></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On 15 April 2016 at 21:29, Tom Goddard <span dir="ltr" class=""><<a href="mailto:goddard@sonic.net" target="_blank" class="">goddard@sonic.net</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word" class="">Hi Jakob,<div class=""><br class=""></div><div class=""> We discussed the excessive STL vertices in atoms and bonds last week and I put a fix into the daily build and release candidate. </div><div class=""><br class=""></div><div class=""><span style="white-space:pre-wrap" class=""> </span><a href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/2016-April/012134.html" target="_blank" class="">http://plato.cgl.ucsf.edu/pipermail/chimera-users/2016-April/012134.html</a></div><div class=""><br class=""></div><div class="">Apparently you are not using those versions since your images show the high vertex density. I’ve attached an image using the current Chimera release candidate that shows reasonable vertex density.</div><div class=""><br class=""></div><div class=""> Unfortunately eliminating internal structures and stitching together meshes for atoms, bonds and ribbons at the seams is very difficult. Yes $10000 CAD software packages can do it but we don’t have the resources to solve that problem. Since every 3d printer has to deal with this problem I expect the printer software to be able to handle it, but perhaps it is too hard a problem for the 3d printer companies as well. Perhaps there is free software that can eliminate internal structures and stitch mesh intersecting edges together, I have not researched it — I’d start looking at MeshLab.</div><div class=""><br class=""></div><div class=""><span style="white-space:pre-wrap" class=""> </span>Tom</div><div class=""><br class=""></div><div class=""><span id="cid:74C2A79B-CEC3-4A5F-8990-39DF7EEB87EC@cgl.ucsf.edu"><stl_mesh.png></span><br class=""><div class=""><blockquote type="cite" class=""><span class=""><div class="">On Apr 15, 2016, at 4:33 AM, Jakob Suckale wrote:</div><br class=""></span><div class=""><div dir="ltr" class=""><span class="">Dear Chimera developers,<div class=""><br class=""></div><div class="">Chimera has the great feature of STL export, very useful for 3D printing models for research and teaching. May I make two suggestion to improve this feature even further.</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">1 - Remove invisible internal and therefore unnecessary structures.</div><div class=""><br class=""></div><div class="">Chimera generates a lot of internal structures that complicate printing and are pointless for STLs. This includes inside surfaces at the end of ribbon cartoons (red below).</div></span><div class=""><span class=""><Screen Shot 2016-04-15 at 13.24.44.png></span> </div><span class=""><div class="">as well as copious amounts of invisible internal surfaces for wire and ball and stick models.</div></span><div class=""><span class=""><Screen Shot 2016-04-15 at 13.27.36.png></span><br class=""></div><span class=""><div class="">If these were automatically removed, STLs would not only be much smaller but also much easier to print without remashing.</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">2 - Reduce the number of vertices for atom models. </div><div class=""><br class=""></div><div class="">Ribbon conversion to vertices is already good, but as can bee seen above atom models are converted using far too many vertices inflating the resulting STL files. I'm aware that this has been discussed and listed previously as a bug but the problem remains and makes for difficult to use STLs and bad 3D prints.</div><div class=""><br class=""></div><div class="">Best regards,<br class=""><br class=""><br class=""></div><div class="">Jakob Suckale, PhD<br class="">Lecturer in Biochemistry<br class="">University of Tübingen<br class=""><a href="tel:%2B49-7071-29-73363" value="+4970712973363" target="_blank" class="">+49-7071-29-73363</a></div></span></div>
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