<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 Anes,<div class=""><br class=""></div><div class=""> If you get an experimental EM map from say the EM Databank it already has the correct voxel size (ie grid spacing) and will not have voxel size 1. Usually they choose a voxel size about 1/3 of map resolution. If this is your situation you don't want to change the voxel size in Chimera -- that simply rescales the map and then alpha helices won't be the correct size in Angstroms. Instead you want to resample the map on a grid that has voxel size 1.0 Angstrom. This is a pain to do in Chimera but is very easy in our newer program ChimeraX.</div><div class=""><br class=""></div><div class=""> In ChimeraX you can do it with the "volume resample" command, for example,</div><div class=""><br class=""></div><div class=""><div><span class="Apple-tab-span" style="white-space:pre"> </span>open 20309 from emdb</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>vol resample #1 spacing 1.0</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>save newmap.mrc model #2</div><div><br class=""></div><div><a href="https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#resample" class="">https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#resample</a></div><div><br class=""></div><div>If you resample high resolution maps with voxel size say 0.6 Angstroms you may get somewhat noisy appearance on a 1.0 Angstrom grid and you may want to smooth the map before resampling with the "volume gaussian" command.</div><div><br class=""></div><div> Tom</div><div><br class=""></div><div><br class=""><blockquote type="cite" class=""><div class="">On Mar 15, 2020, at 12:18 PM, Ouadou, Anes (MU-Student) <<a href="mailto:aomqc@mail.missouri.edu" class="">aomqc@mail.missouri.edu</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="">Hello,</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="">I am using cryo-em density maps to create a deep learning model that detects C-alpha atoms. the model I trained uses maps with voxel size of 1x1x1 A. Experimental maps come in different voxel sizes. I found that I can change the voxel size using the option "model-spec". However, I looked everywhere in Chimera menu bar but could not find "model-spec". can you please show me where to find it. I am also open to any other suggestion to change voxel size.</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="">Regards</div><div 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=""><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><br class=""></div><div id="Signature" class=""><div id="divtagdefaultwrapper" dir="ltr" style="font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols;" class=""><div style="margin-top: 0px; margin-bottom: 0px;" class=""><b class="">Anes Ouadou</b><span class=""><b class=""> </b> </span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class="">CS PhD Student<span class=""> </span></span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class=""><span class="">University of Missouri-Columbia</span></span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class=""><span class=""><a href="mailto:aomqc@mail.missouri.edu" class="">aomqc@mail.missouri.edu</a><span class=""> </span></span></span></div><div style="margin-top: 0px; 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