<div dir="ltr">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><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">goddard@sonic.net</a>> wrote:<br></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;">Hi Shruthi,<div><br></div><div> 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><br></div><div><span style="white-space:pre-wrap"> </span>Tom</div><div><br><div><br><blockquote type="cite"><div>On Feb 21, 2022, at 8:27 PM, Shruthi Viswanath via Chimera-users <<a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank">chimera-users@cgl.ucsf.edu</a>> wrote:</div><br><div><div dir="ltr"><div class="gmail_quote"><div dir="ltr" class="gmail_attr"><span style="color:rgb(51,51,51);font-size:14.6667px">Hello Chimera team, </span><br></div><div dir="ltr"><p style="color:rgb(51,51,51);font-size:14.6667px">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">Thanks very much</p><p style="color:rgb(51,51,51);font-size:14.6667px">Shruthi</p><div style="color:rgb(51,51,51);font-size:14.6667px">--<br><div style="margin:0px;padding:0px;font-family:monospace">Shruthi Viswanath<br>Reader F (Assistant Professor), National Center for Biological Sciences (NCBS)</div><div style="margin:0px;padding:0px;font-family:monospace">GKVK, Bellary Road, Bangalore, India 560065<br>Tel: +91 80 6717-6152<br>Email: <a href="mailto:shruthiv@ncbs.res.in" rel="noreferrer" style="color:rgb(0,105,166)" target="_blank">shruthiv@ncbs.res.in</a> </div><div style="margin:0px;padding:0px;font-family:monospace">Web: <a href="https://www.ncbs.res.in/faculty/shruthi" rel="noreferrer" style="color:rgb(0,105,166)" target="_blank">https://www.ncbs.res.in/faculty/shruthi</a></div></div></div>
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