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

[Tom Goddard]

Hi Shruthi,

  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.

  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,

	vop scale #0 shift 3.2

documentation

	https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#scale <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#scale>

  Tom


> On Feb 22, 2022, at 11:46 AM, Shruthi Viswanath <shruthi.viswanath at gmail.com> wrote:
> 
> 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 <mailto: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 <mailto: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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> 
> <increased_threshold_volume_viewer.png><full_segmentation_plus_new_region_volume_viewer.png>

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