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

[Tom Goddard]

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