Create extraction job of neighbouring particle from 3D reconstruction

Features and Functionality
1

Dear Cryosparc team,

Would it be possible to add a tab on the extraction job with coordinates to extract particles next to the 3D reconstruction?

I hope the request is clear.

Best regards,
Nuno

2

For us to better understand your request, please can provide more details on

  • whether the feature should affect input to or output from a particle extraction job
  • the relationship between the particles, coordinates and 3D reconstruction
  • the specific use case and how the added feature would facilitate processing therein

With 3D reconstruction, do you mean the volume output by 3D reconstruction or the 3D construction process/job type?

3

Dear @wtempel

Thanks for your reply.

Reply: With 3D reconstruction, do you mean the volume output by 3D reconstruction or the 3D construction process/job type?

I mean from the volume output. I will try to explain it in my following example:

image
image1160Ă—962 127 KB

In this 3D reconstruction volume I have a neighboring ribosome particle. Instead of increasing the box size to reconstruct them together I would like to extract the particles that are next to this one to reconstruct the neighbor ribosome.

The feature as I see it should affect the input to from the extraction job. For example, Relion has an option for re-extract refined particles and you can re-center refined coordinates in X,Y,Z.

Thanks once again for your quick reply.

Best,
Nuno

4

Hi @nbustorff,

This can be done via the Volume Alignment Tools job. This allows one to re-center a volume and particles on arbitrary x, y, z coordinates. You’ll have to find the coordinates of the center of the neighbouring domain of interest on the 3D reconstruction. These coordinates can be input into the job (the expected convention is that they are indexed from the corner of the volume). The output particles can be put through an extraction job with re-centering enabled, to get particles that have been re-centered on the neighbouring domain.

Best,
Michael

3 Likes
5

Thanks a lot.

Best,
Nuno

6

Do I need to add location from extraction job?

image
image1548Ă—334 61.8 KB

7

The volume alignment tools job only needs the alignments3D from the refined particles, but the extraction job needs the location and alignments3D.

8

Exactly. The only job that has location is the extraction job type right? all other jobs don’t have it as I understood. So for the re-extraction job, I use the particles from the alignment tools job which have the alignments3D and the location “suboutput” comes from the first extraction job. Did I get it right?

Thanks for all the support

Best,
Nuno

9

Hi @nbustorff ,

Could you post a screenshot of the outputs tab of the volume alignment tools job, showing the result group associated with the particles? With the particles that were output from the volume alignment tools job, i’d expect you to see that particles have the “location” group being passed-through, thus there shouldn’t be any need to use the original location result group from the original extraction job.

Best,
Michael

10

Hi @mmclean,

image
image1897Ă—735 135 KB

I checked all outputs from 3D reconstructions, 2D classifications, and only found location group in the extraction job. All particles in these jobs come from a downsample job.

From the next screen shot it looks like the downsample job didn’t take the location of the particles as input

image
image1894Ă—321 36.4 KB

I don’t know if it was just a bug.

I always drag and drop the full particle output from the previous job.

I cloned the job now just to see what it would take as an input.

My job cloned - old input:
image

My job cloned - new input:
image

Thnaks for your help!

Best,
Nuno