<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 Shruthi,<div class=""><br class=""></div><div class=""> EMDB 2329 is quite strange in that the values outside the structure are -3 and lower and the values inside the structure are -3 to 1.44. Usually the values outside the structure are mostly at 0. This may be confusing Segger. The UCSF Chimera team did not write Segger -- it was written by Greg Pintilie and I do not know if it expects map values that it extracts for segmented regions to be above 0.</div><div class=""><br class=""></div><div class=""> At any rate, you can probably fix this weird behavior by adding about 3.2 to the original EMDB map so the structure values are above 0, rather than above -3.2 using the vop scale command, for example,</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>vop scale #0 shift 3.2<br class=""><div><br class=""></div><div>documentation</div><div><br class=""></div><div><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#scale" class="">https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#scale</a></div><div><br class=""></div><div> Tom</div><div><br class=""></div><div><br class=""></div><div><blockquote type="cite" class=""><div class="">On Feb 22, 2022, at 11:46 AM, Shruthi Viswanath <<a href="mailto:shruthi.viswanath@gmail.com" class="">shruthi.viswanath@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Thanks Tom. When I adjust the threshold to a higher level only a small part of the segmented density is seen; it does not look like the segmented region at all. Attaching screenshots of the volume viewer with the full segmentation and with the threshold increased. </div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Feb 23, 2022 at 1:03 AM Tom Goddard <<a href="mailto:goddard@sonic.net" class="">goddard@sonic.net</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="overflow-wrap: break-word;" class="">Hi Shruthi,<div class=""><br class=""></div><div class=""> It is probably because Chimera did not set the threshold level for showing that map to a reasonable value. Try adjusting the threshold for that new map to a higher level. If you want more help with it, send a screenshot of what the Volume Viewer window looks like, showing the histogram of the map values and the threshold level.</div><div class=""><br class=""></div><div class=""><span style="white-space:pre-wrap" class=""> </span>Tom</div><div class=""><br class=""><div class=""><br class=""><blockquote type="cite" class=""><div class="">On Feb 21, 2022, at 8:27 PM, Shruthi Viswanath via Chimera-users <<a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank" class="">chimera-users@cgl.ucsf.edu</a>> wrote:</div><br class=""><div class=""><div dir="ltr" class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr"><span style="color:rgb(51,51,51);font-size:14.6667px" class="">Hello Chimera team, </span><br class=""></div><div dir="ltr" class=""><p style="color:rgb(51,51,51);font-size:14.6667px" class="">We have a problem with saving segmented regions from EMD 2329 using Segger. When we segment one of the 9 spokes from this EM map and try to do File -> save selected regions to .mrc from the Segger window it displays a box around the selected region (see screenshot) and the saved .mrc file just shows a small blob and does not look like the original selected region. Could it be because of the lower than usual density range of this particular map? </p><p style="color:rgb(51,51,51);font-size:14.6667px" class="">Thanks very much</p><p style="color:rgb(51,51,51);font-size:14.6667px" class="">Shruthi</p><div style="color:rgb(51,51,51);font-size:14.6667px" class="">--<br class=""><div style="margin:0px;padding:0px;font-family:monospace" class="">Shruthi Viswanath<br class="">Reader F (Assistant Professor), National Center for Biological Sciences (NCBS)</div><div style="margin:0px;padding:0px;font-family:monospace" class="">GKVK, Bellary Road, Bangalore, India 560065<br class="">Tel: +91 80 6717-6152<br class="">Email: <a href="mailto:shruthiv@ncbs.res.in" rel="noreferrer" style="color:rgb(0,105,166)" target="_blank" class="">shruthiv@ncbs.res.in</a> </div><div style="margin:0px;padding:0px;font-family:monospace" class="">Web: <a href="https://www.ncbs.res.in/faculty/shruthi" rel="noreferrer" style="color:rgb(0,105,166)" target="_blank" class="">https://www.ncbs.res.in/faculty/shruthi</a></div></div></div>
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<span id="gmail-m_-6109050917316040184cid:f_kzxmiybo0" class=""><Screenshot 2022-02-22 at 8.51.03 AM.png></span>_______________________________________________<br class="">Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" target="_blank" class="">Chimera-users@cgl.ucsf.edu</a><br class="">Manage subscription: <a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users" target="_blank" class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users</a><br class=""></div></blockquote></div><br class=""></div></div></blockquote></div>
<span id="cid:f_kzyjg0u70"><increased_threshold_volume_viewer.png></span><span id="cid:f_kzyjg0uy1"><full_segmentation_plus_new_region_volume_viewer.png></span></div></blockquote></div><br class=""></div></body></html>