[Chimera-users] Saving segmented regions from EM map not working

[Shruthi Viswanath]

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 at 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 at 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 at ncbs.res.in
> Web: https://www.ncbs.res.in/faculty/shruthi
> <Screenshot 2022-02-22 at 8.51.03 AM.png>
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