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. On Wed, Feb 23, 2022 at 1:03 AM Tom Goddard <goddard@sonic.net> wrote:
Hi Shruthi,
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.
Tom
On Feb 21, 2022, at 8:27 PM, Shruthi Viswanath via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Hello Chimera team,
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?
Thanks very much
Shruthi -- Shruthi Viswanath Reader F (Assistant Professor), National Center for Biological Sciences (NCBS) GKVK, Bellary Road, Bangalore, India 560065 Tel: +91 80 6717-6152 Email: shruthiv@ncbs.res.in Web: https://www.ncbs.res.in/faculty/shruthi <Screenshot 2022-02-22 at 8.51.03 AM.png> _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
