<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div class="">Hi Jon,</div><div class=""><br class=""></div><div class=""> The command to show a subregion of a volume looks like</div><div class=""><br class=""></div><span class="Apple-tab-span" style="white-space:pre"> </span>volume #1 region 0,0,0,85,100,50<div class=""><br class=""></div><div class="">where the 6 numbers are the two corners in grid index units. You would need to look at the size of your grid (shown in Volume Viewer) and specify a smaller size in this command. But using a command is a pretty difficult approach to cropping the volume, more commonly it would be done interactively with the mouse using the Volume Viewer menu Features / Subregion Selection.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html" class="">https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html</a></div><div class=""><br class=""></div><div class=""> Tom</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Feb 4, 2019, at 2:04 PM, Mauser, Jonathon wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="WordSection1" style="page: WordSection1; caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Thank you, Tom. What commands would I need to simply reduce the size of a density/surface model bounding box?<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div class=""><div style="border-style: solid none none; border-top-width: 1pt; border-top-color: rgb(225, 225, 225); padding: 3pt 0in 0in;" class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><b class="">From:</b><span class="Apple-converted-space"> </span>Tom Goddard<br class=""><b class="">Sent:</b><span class="Apple-converted-space"> </span>Monday, February 4, 2019 3:52 PM<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span>Mauser, Jonathon <br class=""><b class="">Cc:</b><span class="Apple-converted-space"> </span><a href="mailto:chimera-users@cgl.ucsf.edu" style="color: purple; text-decoration: underline;" class="">chimera-users@cgl.ucsf.edu</a><span class="Apple-converted-space"> </span>BB <<a href="mailto:chimera-users@cgl.ucsf.edu" style="color: purple; text-decoration: underline;" class="">chimera-users@cgl.ucsf.edu</a>><br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [Chimera-users] Slicing/Subdividing Models in Chimera<o:p class=""></o:p></div></div></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Hi Jon,<o:p class=""></o:p></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> You won’t be able to get STL of a clipped molecule from Chimera — as you observed you get the full molecule instead. The problem is that clip planes are just a graphical operation where the graphics decides not to display some of the pixels that would be behind or in front of a clip plane. But the STL format is a list of triangles. To make a list of triangles all the triangles cut by the clipping plane would have to be trimmed and the out of view triangles and partial triangles thrown away. Chimera does not do that. Often that is not enough as 3D printer software often requires the triangles are joined at their edges to form a closed mesh, and the tiniest gap causes the 3d printer software to fail (observed with old Catalyst software and uPrint printers). Clipping and getting closed triangles requires even fancier software — this is typical of mechanical engineering CAD software.<o:p class=""></o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> The one thing you can do to slice is and 3D print is use a surface calculated from a density map, and reduce the bounding box of the density map. The Chimera molmap command makes such density maps from molecules. But it won’t give ribbon or ball-and-stick type appearances.<o:p class=""></o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> Lastly when cutting molecules you are likely to produce many disconnected fragments which will simply fall apart if you try to 3D print them after you dissolve the support material.<o:p class=""></o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span class="apple-tab-span"> <span class="Apple-converted-space"> </span></span>Tom<o:p class=""></o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><br class=""><br class=""><o:p class=""></o:p></div><blockquote style="margin-top: 5pt; margin-bottom: 5pt;" class=""><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">On Feb 4, 2019, at 8:38 AM, Mauser, Jonathon wrote:<o:p class=""></o:p></div></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div class=""><div class=""><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Hello,<o:p class=""></o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">I am working on developing a new suite of flexible multimedia 3D printed protein models using Chimera to process to .stl. I am trying to make a sort of “anatomical” cutaway of an enzyme complex where I can slice the model in chimera along a certain plane and print the sections with caps, but am running into problems.<span class="apple-converted-space"> </span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">I have tried simply clipping into the model, which does essentially what I would like to do, but I don’t know how to delete everything that I’ve clipped out of the model. When I export my scene, it still exports the whole model instead of the clipped depiction. Ideally, I would like to just cut the pdb in half to start with more advanced cutaways coming later. Do you have any idea how this might be accomplished?<o:p class=""></o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Thank you!<o:p class=""></o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Jon<o:p class=""></o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><b class=""><span style="font-size: 10pt; font-family: Tahoma, sans-serif;" class="">Jonathon Mauser, Ph.D.</span></b><o:p class=""></o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 10pt; font-family: Tahoma, sans-serif;" class="">Assistant Professor</span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 10pt; font-family: Tahoma, sans-serif;" class="">Department of Chemistry</span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 10pt; font-family: Tahoma, sans-serif;" class="">Winona State University</span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 10pt; font-family: Tahoma, sans-serif;" class="">Office: Pasteur Hall 330</span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 10pt; font-family: Tahoma, sans-serif;" class="">P: 507-457-5874</span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 10pt; font-family: Tahoma, sans-serif;" class="">E:<span class="apple-converted-space"> </span><a href="mailto:jmauser@winona.edu" style="color: purple; text-decoration: underline;" class=""><span style="color: rgb(5, 99, 193);" class="">jmauser@winona.edu</span></a></span><o:p class=""></o:p></div></div></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">_______________________________________________<br class="">Chimera-users mailing list:<span class="Apple-converted-space"> </span><a href="mailto:Chimera-users@cgl.ucsf.edu" style="color: purple; text-decoration: underline;" class="">Chimera-users@cgl.ucsf.edu</a><br class="">Manage subscription:<span class="Apple-converted-space"> </span><a href="https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.ucsf.edu%2Fmailman%2Flistinfo%2Fchimera-users&data=02%7C01%7Cjmauser%40winona.edu%7Cfbe5a4beeb5e46b1d42108d68aeaf4ea%7C5011c7c60ab446ab9ef4fae74a921a7f%7C0%7C1%7C636849139071134499&sdata=AfTxGOgumPo1V7dYcrF%2FX1gZsdPX8Vr3%2FtfNdz3mySs%3D&reserved=0" style="color: purple; text-decoration: underline;" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a></div></div></blockquote></div></div></div></div></blockquote></div><br class=""></div></body></html>