<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="">Dear Tom, dear Elaine,<div class=""><br class=""></div><div class="">Thanks a lot to both of you for the prompt and detailed reply. Elaine’s tip goes towards what I would like to achieve, however I think the issue is how ChimeraX reads the input. I managed to get this rendering with the software Dragonfly (attached the screenshot) where somehow the zeros are displayed in 3D as “empty space”. In ChimeraX though they are displayed as black pixels. I also adapted your command line Tom (<i class="">volume #1 style image region 120,0,0,1346,1400,1449 step 1,1,1 colormode l16 proj 2d-z showOutlineBox true outlineBoxRgb white</i>) and I still get the similar output (please see attached a snapshot). I converted the input .tiff frames as a single .mrc volume (header reports map mode=0) but the issue still persists. </div><div class=""><br class=""></div><div class="">Do you have further suggestions?</div><div class="">I am using ChimeraX (version 1.4rc202205200050 (2022-05-20)) on a windows desktop. </div><div class=""><br class=""></div><div class="">Thank you,</div><div class=""><br class=""></div><div class="">Edoardo</div><div class=""><br class=""></div><div class=""><img apple-inline="yes" id="D0E209B2-5760-4933-836E-052067A8F0DB" src="cid:ECAAE619-A2F0-4674-B4B7-096379D12818@embl.de" class=""><img apple-inline="yes" id="4CEE1005-843A-4789-891A-670AB06F497C" src="cid:421FE62C-2A73-4860-B1F2-08448719643B@embl.de" class=""><br class=""><div class="">
<div 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; text-decoration: none; caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);">------------------------------------------------------<br class="">Dr. Edoardo D'Imprima<br class="">Postdoctoral fellow<br class="">Structural and Computational Biology Unit<br class="">EMBL Heidelberg - Mahamid Group<br class="">Meyerhofstraße 1<br class="">69117 Heidelberg<br class="">Germany<br class=""><br class="">Phone: +49 6221 387-8531<br class=""></div><span style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); 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; text-decoration: none;"></span><br class="Apple-interchange-newline"><span><img apple-inline="yes" id="93B7C8D0-F5B0-46B4-8801-9DAAEA49E144" src="cid:5c6ab8d1e07d81264d7b9723c4334399" class=""></span>
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<div><br class=""><blockquote type="cite" class=""><div class="">On 24. May 2022, at 19:28, Tom Goddard <<a href="mailto:goddard@sonic.net" class="">goddard@sonic.net</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Edoardo,<div class=""><br class=""></div><div class=""> Elaine's example shows how to make the middle solid box image of your figure. To make the left image which shows 4 slices you can do something like this</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>open 11638 from emdb</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>set bgColor white</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>volume #1 style image region 0,0,50,256,256,200 step 1,1,50 colormode l8 proj 2d-z showOutlineBox true outlineBoxRgb black<br class=""><div class=""><br class=""></div><div class="">Here's an explanation of the options in that long volume command. "style image" means gray scale rendering instead of surface. "region 0,0,50,256,256,200" gives the bounds of the region and says to start at z plane 50 and end at z plane 200, the six values xmin,ymin,zmin,xmax,ymax,zmax. The "step 1,1,50" means show every voxel along x and y axes, but only every 50th plane in z. The "colormode l8" means make the planes opaque. The "proj 2d-z" means show the planes of the volume as 2d planes perpendicular to the z axis. The "showOutlineBox true" means to draw the lines outlining the data and "outlineBoxRgb black" makes the line color black. Documentation here</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/chimerax/docs/user/commands/volume.html#dispsolid" class="">https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#dispsolid</a></div><div class=""><br class=""></div><div class=""> A simpler approach would be just to use the Volume Viewer panel and set the style (menu above the histogram) to "plane". That will show a scrollbar that lets you flip through the planes (you may have to scroll the volume viewer panel to see the horizontal scrollbar below the histogram). Then without rotating you just choose the planes you want and save an image of each plane with background transparency ("save plane1.png width 1500 transparent true") and stack them in photo editing program.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div class=""><span id="cid:24A30FA5-8A4A-4517-8333-E2DFDA644E67"><emd11638_planes.png></span></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><blockquote type="cite" class=""><div class="">On May 24, 2022, at 9:18 AM, Elaine Meng via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Edoardo,<div class="">I believe you can do this by choosing "box" display from the rightmost pulldown in the Volume Viewer dialog. See the screenshot attached below.</div><div class=""><br class=""></div><div class="">Volume Viewer dialog settings:</div><div class=""><<a href="https://rbvi.ucsf.edu/chimerax/docs/user/tools/volumeviewer.html" class="">https://rbvi.ucsf.edu/chimerax/docs/user/tools/volumeviewer.html</a>></div><div class=""><br class=""></div><div class="">I hope this helps,</div><div class="">Elaine<br class=""><div class="">-----<br class="">Elaine C. Meng, Ph.D. <br class="">UCSF Chimera(X) team<br class="">Department of Pharmaceutical Chemistry<br class="">University of California, San Francisco<br class=""><br class=""><span id="cid:6F591EDD-D8FE-45A5-893A-75D127430A95@gateway.sonic.net" class=""><Screen Shot 2022-05-24 at 9.15.15 AM.png></span><br class=""><br class=""></div><br class=""><blockquote type="cite" class="">On May 24, 2022, at 8:00 AM, Edoardo D Imprima via ChimeraX-users <chimerax-<a href="mailto:users@cgl.ucsf.edu" class="">users@cgl.ucsf.edu</a>> wrote:<br class=""><br class="">Hello,<br class="">Could you please tell me how to display fib-sem tomography data as a compact volume that can be navigated by sliding planes? The data consists of a series of frames that I can convert as .mrc volume or .mrcs stack. I attach a snapshot taken from a review that illustrates (middle panel) the visualisation I would like to obtain. The medical-image panel in ChimeraX is very handy however, the “full” option shows the volume while I need to display the planes of each side to slice through them. <br class="">Looking forward to your feedback,<br class="">Best wishes,<br class="">Edoardo<br class=""></blockquote><br class=""></div></div>_______________________________________________<br class="">ChimeraX-users mailing list<br class=""><a href="mailto:ChimeraX-users@cgl.ucsf.edu" class="">ChimeraX-users@cgl.ucsf.edu</a><br class="">Manage subscription:<br class=""><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a><br class=""></div></blockquote></div><br class=""></div></div></div></blockquote></div><br class=""></div></body></html>