<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Ilhan,<div class=""><br class=""></div><div class=""> The ChimeraX source code for map outline boxes is Python and is in the ChimeraX distribution.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>on Windows: chimerax/bin/Lib/site-packages/chimerax/map/volume.py</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>on macOS: ChimeraX.app/Contents/lib/python3.7/site-packages/chimerax/map/volume.py</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>on Linux: chimerax/lib/python3.7/site-packages/chimerax/map/volume.py</div><div class=""><br class=""></div><div class="">A trick to display an outline box mesh is make a copy of your map (one time point, "save grid.mrc model #1.1") and open it, display mesh style and set the threshold level to less than the lowest value in the map. Here's what I see for some lightsheet microscopy of an immune cell. Ugly, mesh has triangles. But also having a whole box of mesh lines looks busy.</div><div class=""><br class=""></div><div class=""><img apple-inline="yes" id="BEF7B6FB-77E5-4945-BB95-7B7FBAB476E7" width="414" height="376" src="cid:424E8BEE-B815-4025-B492-77540AF005FA" class=""></div><div class=""><br class=""></div><div class="">So I made a single plane with ChimeraX command "shape rectangle", positioned it over the microscopy with move selected mouse mode, and showed it as mesh style with "surface style #3 mesh". Still has the ugly diagonal lines.</div><div class=""><br class=""></div><div class=""><img apple-inline="yes" id="C01C9DCE-83C1-49CA-9CD7-BDFAC810E466" width="400" height="366.018" src="cid:5FBA9942-3861-491B-8F94-43B217F9AA2F" class=""></div><div class=""><br class=""></div><div class="">So I wrote some Python to hide the diagonals. I put this on the ChimeraX recipes web site as an example.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://rbvi.github.io/chimerax-recipes/hide_diagonals/hide_diagonals.html" class="">https://rbvi.github.io/chimerax-recipes/hide_diagonals/hide_diagonals.html</a></div><div class=""><br class=""></div><div class="">and I will try to put it into the ChimeraX distribution today as the "surface squaremesh" command.</div><div class=""><br class=""></div><div class=""><img apple-inline="yes" id="2FCD43AE-DD3D-44A6-B430-EF10D28893FA" width="400" height="388.827" src="cid:F66DC9DD-8F55-4BE0-BC8A-E7348E66FF5E" class=""></div><div class=""><br class=""></div><div class="">This last view I used "camera ortho" to get orthographic projection. The standard ChimeraX camera mode is perspective projection and makes this closer look bigger which is not good if you want to measure distances.</div><div class=""><br class=""></div><div class="">You could also possibly use "shape rectangle" to make a scale bar.</div><div class=""><br class=""></div><div class="">If you still want access to the ChimeraX GitHub repository, send me your github user name and I can add you.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Oct 19, 2020, at 4:00 AM, Tomris, I. (Ilhan) <<a href="mailto:i.tomris@uu.nl" class="">i.tomris@uu.nl</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div style="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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">Dear sir/madam,</div><div style="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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><br class=""></div><div style="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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">At the moment I am utitilizing ChimeraX to render 3D images of lightsheet data I have obtained (see attachment of 3D render). It is a pretty nice software package, although there is something I would like to implement into chimerax. A bounding box/outline box with gridpoints on it to indicate the size of the rendered volume, additionally I would also like to implement a scalebar of some sort. Hence I was wondering whether I could get access to the git repository so I could attempt to use the "Outline box" already present and put grid points on it?</div><div style="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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><br class=""></div><div style="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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><span id="cid:ab15abd2-e188-42fa-ae88-eedbeae317dd"><image.png></span> </div><div style="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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">Kind regards,</div><div style="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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><br class=""></div><div style="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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">Ilhan</div><span id="cid:1AF0E6FE-B3A9-449D-B7DE-FED95C706873"><chimerax render.mp4></span><span style="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; float: none; display: inline !important;" class="">_______________________________________________</span><br style="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;" class=""><span style="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; float: none; display: inline !important;" class="">ChimeraX-users mailing list</span><br style="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;" class=""><a href="mailto:ChimeraX-users@cgl.ucsf.edu" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">ChimeraX-users@cgl.ucsf.edu</a><br style="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;" class=""><span style="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; float: none; display: inline !important;" class="">Manage subscription:</span><br style="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;" class=""><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a></div></blockquote></div><br class=""></div></body></html>