Saving segmented regions from EM map not working
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
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 mailto:shruthiv@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>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
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
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@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@sonic.net mailto: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 mailto: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 mailto:shruthiv@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>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu mailto:Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
<increased_threshold_volume_viewer.png><full_segmentation_plus_new_region_volume_viewer.png>
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 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... 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@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 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@gmail.com mailto:shruthi.viswanath@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@sonic.net mailto: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 mailto: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 mailto:shruthiv@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>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu mailto:Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
<increased_threshold_volume_viewer.png><full_segmentation_plus_new_region_volume_viewer.png>
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@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...
Greg
On Feb 22, 2022, at 3:33 PM, Tom Goddard goddard@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@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@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
<increased_threshold_volume_viewer.png>
<full_segmentation_plus_new_region_volume_viewer.png>
participants (3)
-
Greg Pintilie -
Shruthi Viswanath -
Tom Goddard