<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="">Hi Andre,<div class=""><br class=""></div><div class=""> The Segger segmentation tool was written by Greg Pintilie, not by the UCSF ChimeraX team. I moved part of it from Chimera to ChimeraX hoping to convince Greg to switch from Chimera to ChimeraX, but so far no luck. Chimera has not been developed for 5 years except for critical fixes so it is too bad most of the Segger tools are not in ChimeraX.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Feb 4, 2022, at 11:40 AM, Andre LB Ambrosio 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 dir="ltr" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 18px; 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="">Dear Elaine, many thanks for this. <br class=""><div class="">Sorry for overlooking the help page.</div><div class="">I ended up installing Chimera to use the "extract densities" option, as I had difficulties matching the exact box dimensions of the new map to that of the original map when using the volume mask command.</div><div class="">I can move forward with local refinement now!</div><div class="">Thank you again.</div></div><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 18px; 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 class="gmail_quote" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 18px; 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 dir="ltr" class="gmail_attr">Em sex., 4 de fev. de 2022 às 13:55, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" target="_blank" class="">meng@cgl.ucsf.edu</a>> escreveu:<br class=""></div><blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-style: solid; border-left-color: rgb(204, 204, 204); padding-left: 1ex;"><div class="">Hi Andre,<div class="">According to the ChimeraX help page for the Segment Map tool, menu "Regions... Extract densities" is not yet implemented:</div><div class=""><<a href="https://rbvi.ucsf.edu/chimerax/docs/user/tools/segment.html#menu-regions" target="_blank" class="">https://rbvi.ucsf.edu/chimerax/docs/user/tools/segment.html#menu-regions</a>></div><div class=""><br class=""></div><div class="">However, I think you can find the model number of the surface (group) that you want by looking in the Model Panel, and then extract that part of the density map using the "volume mask" command:</div><div class=""><<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#mask" target="_blank" class="">https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#mask</a>></div><div class=""><br class=""></div><div class="">For example, in the attached screen shot of a fake example I made up, I have several segmentation regions. The overall segmentation model is #3 and I can see that the one I have selected is the green blob in the middle, which is named 285 in the model panel and is model #3.1. The density map is #2. So (for example) to get density of map #2 inside surface #3.1 to create new map model #5 I can use command</div><div class=""><br class=""></div><div class="">volume mask #2 surfaces #3.1 modelId #5</div><div class=""><br class=""></div><div class="">There are other options of the command, see the link above. Then you can save map #5 to a file with "save" command:</div><div class=""><<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#map" target="_blank" class="">https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#map</a>></div><div class=""><br class=""></div><div class="">The alternative is to use Segger in Chimera, where I believe that the extract densities option in the Regions menu is implemented:</div><div class=""><<a href="https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/segger/segment.html#menu-regions" target="_blank" class="">https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/segger/segment.html#menu-regions</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:17ec63990db793352ed1"><Screen Shot 2022-02-04 at 8.47.59 AM.png></span><br class=""><br class=""></div><br class=""><blockquote type="cite" class="">On Feb 4, 2022, at 7:55 AM, Andre LB Ambrosio via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:<br class=""><br class="">Dear all, probably a silly question:<br class="">I want to generate a mask o ChimeraX to use later on a local refinement job elsewhere.<br class="">I managed to segment the cryoEM map and group the regions of interest. <br class="">However, the "Extract densities" option is unavailable on the "Regions" menu.<br class="">Likewise, these are unavailable on "Other tools" shortcuts options: Extract, iSeg, ProMod, and ModelZ.<br class="">Please, what am I missing?<br class="">I appreciate any help you can provide.<br class=""></blockquote><br class=""></div></div></blockquote></div><br clear="all" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 18px; 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="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 18px; 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=""><br class=""></div><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 18px; 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 class="Apple-converted-space"> </span></span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 18px; 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 dir="ltr" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 18px; 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 dir="ltr" class=""><div class="">Andre LB Ambrosio</div><div class="">Associate Professor, IFSC/USP - Brazil</div><div class=""><a href="http://www.ifsc.usp.br/alba" target="_blank" class="">www.ifsc.usp.br/alba</a><br class=""></div></div></div><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; 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