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

[Shruthi Viswanath]

Thanks Tom, that works for us now.
@greg, the threshold was set to author-defined contour level (-3.07) and
segmenting seemed to work fine, we didn't see a box around the entire map.
Thanks, we will use the Extract operation in the new Segger.

On Wed, Feb 23, 2022 at 2:36 AM Greg Pintilie <gregdp at gmail.com> wrote:

>
> The other thing that is strange here is that there are negative values to
> begin with in the extracted map…
>
> The function ‘File -> save selected regions to .mrc' only takes values
> inside segments, which typically only have positive values in them, so I’m
> surprised to see negative values. Could you tell us what the threshold the
> map was when segmenting? I assume it was positive otherwise you would have
> seen a box around the entire map when doing the segmentation.
>
> Looking at the code, the same function seems to use whatever map is
> selected in the Segment map field (top of the Segment Map dialog) to
> extract from, if it’s a different map than the original map (perhaps one of
> the other region maps got selected somehow - I tend to fall into this trap
> myself a lot), it will probably generate nonsense like that - should handle
> this better somehow. So can you check that when you run the function, that
> the original map is selected in that field?
>
> Btw, I’m hoping to switch soon to ChimeraX, but have updated newer
> versions of Segger in Chimera lately with fixes, though you have to install
> it separately from https://github.com/gregdp/segger. In these newer
> versions you may want to try out the ‘Extract’ dialog which gives you a bit
> more control over what is happening when doing this kind of operation:
>
> https://github.com/gregdp/segger/blob/master/tutorials/Segger%20Tutorial%205%20-%20Extract.pdf
>
>
> Greg
>
>
>
>
> On Feb 22, 2022, at 3:33 PM, Tom Goddard <goddard at sonic.net> wrote:
>
> 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
>
>   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> 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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>>
>> <increased_threshold_volume_viewer.png>
> <full_segmentation_plus_new_region_volume_viewer.png>
>
>
>
>
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