Align filament classes vertically in cryosparc 3.0.1

Dmitry · January 30, 2021, 6:09pm

Dear colleagues,

I am using cryoSPARC 3.0.1 for the helical reconstruction.

I would like to ask where/how can I find the “Align filament classes vertically” option in the 2D alignment?

Thank you.

Sincerely,
Dmitry

Pengxin · January 30, 2021, 7:13pm

It is in the 2D classification job.

Dmitry · January 30, 2021, 7:38pm

Unless I am mistaken, but I see no " Align filament classes vertically in the 2D.

Could you please specify more?
Which version of the cryoSPARC you use?

Thank you

Pengxin · January 30, 2021, 7:50pm

I am using V3.

Dmitry · January 30, 2021, 8:25pm

Thank you.
Interestingly my 2D classification menu looks differently.
I really wonder why?

Pengxin · January 30, 2021, 8:34pm

Are the worker and master both v3?

Dmitry · January 30, 2021, 8:44pm

that is what I am going to figure out.
Could you please prompt me the way to do that?

I am a new user.

Thank you.

Pengxin · January 30, 2021, 8:49pm

Several things to try next:

run a job, see whether there is a warning like “worker and master version mismatch”
If the worker and master do not match, update. (There are many topics about how to update)
If the worker and master do match, you can try to restart cryosaprc by typing: cryosparcm restart

Dmitry · January 30, 2021, 8:50pm

Thank you!

Sincerely,
Dmitry

mmclean · January 31, 2021, 12:40am

Hi all,

The “align filament class vertically” switch is a parameter in 2D classification that will simply rotate the 2D classes such that the helical axis is approximately aligned with the y-axis of the images — it is primarily intended for easier visual comparison between classes.

It is an “advanced” parameter, meaning the switch at the top right of the job builder must be activated to see this parameter. This switch is to the right of the “New Job JXX” label - in @Pengxin’s screenshot the advanced switch is on, but in @Dmitry’s screenshot it is off, meaning all of the advanced parameters will be hidden. We are currently in the process of updating our documentation for all jobs to explain parameters like these more closely; for the helical processing specific documentation, you can refer to our guide pages on the subject.

Best,
Michael

Pengxin · January 31, 2021, 12:58am

Thanks for explaining! I never noticed that option.
By the way, I really like the “align filament class vertically” function!

Dmitry · January 31, 2021, 2:42pm

Thank you!
when I enabled the advanced parameter (which for some reason is named “New job XXX”) it appeared that the “Align filament classes” feature was on by default.

Sincerely,
Dmitry

mmclean · February 1, 2021, 4:39pm

Hi @Dmitry,

No problem! If you have picked particles from the filament tracer job (or have otherwise imported particles with the rlnHelicalTubeID field), then 2D classification will recognize that the particles are helical picks, and will enable the parameter by default.

Best,
Michael