e2spt_trajfromrefine.py error

Maia Azubel

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Aug 24, 2021, 7:10:07 PM8/24/21

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Hi Muyuan,

I'm following your tutorial on spt focused refinement.

https://blake.bcm.edu/emanwiki/EMAN2/e2tomo_more

Everything worked fine until I got to e2spt_trajectformrefine.

Command and error below.

Also, once you have the result how do you visualize the motion in Chimera?

Many thanks,
Maia

EMAN 2.91 final ( GITHUB: 2021-03-08 11:36 - commit: 81caed2 )

Your Python version is: 3.7.9

Command

e2spt_trajfromrefine.py --path spt_118 --iter 5

Refine stats saved to spt_118/refinestats_05.txt. The three columns are:

Translation - mean: 23.92 std: 8.02

Rotation - mean: 101.05 std: 62.84

Score - mean: -0.30 std: 0.05

Generating eigen-trajectory...

Eigen values saved to spt_118/eigval_05.txt

Trajectory 0:

Rotation - x: -19.73 y: 1.99 z: -0.70

Translation - x: -10.22 y: 6.34 z: -13.00

Trajectory file written to spt_118/traj_it05eg00.hdf

Trajectory 1:

Rotation - x: -4.74 y: -14.19 z: -14.02

Translation - x: -11.42 y: -1.48 z: -3.08

Trajectory file written to spt_118/traj_it05eg01.hdf

Making averages along trajectories...

[-2. -1. 0. 1. 2.]

Traceback (most recent call last):

File "/programs/x86_64-linux/eman2/2.91/bin/e2spt_trajfromrefine.py", line 163, in <module>

main()

File "/programs/x86_64-linux/eman2/2.91/bin/e2spt_trajfromrefine.py", line 143, in main

dcout={keys[i]:dic00[keys[i]] for i in idx}

File "/programs/x86_64-linux/eman2/2.91/bin/e2spt_trajfromrefine.py", line 143, in <dictcomp>

dcout={keys[i]:dic00[keys[i]] for i in idx}

NameError: free variable 'dic00' referenced before assignment in enclosing scope

Muyuan Chen

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Aug 24, 2021, 7:37:02 PM8/24/21

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I think it is expecting another particles_params_xx.json file to be input through --parminit option, which would be the alignment parameters before the focused refinement. In theory, if the particles are extracted from an existing alignment, it should also work without --parminit. However, it seems that there is a bug in the version you are on, that triggers the error you have. Unfortunately I cannot fix the bug on my side, because the program has been updated significantly since March, to work with the new spt pipeline, and I have not made it compatible with previous versions yet. So the choices are: 1. find the json file for the global alignment and use as input. 2. edit the program on your side locally, simply changing "dic00" to "dic" in that line (File "/programs/x86_64-linux/eman2/2.91/bin/e2spt_trajfromrefine.py", line 143, in main
) should work.

To visualize, I use the volume series function in chimera. I have only recently noticed that it may have issue ordering the movie correctly if you open a long enough one (>10 frames). Still trying to figure out the best solution to that...

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Maia Azubel

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Aug 25, 2021, 2:42:43 PM8/25/21

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Thanks for the fast response, Muyuan!

I tried

e2spt_trajfromrefine.py --path spt_118 --iter 5 --parminit spt_118/particle_parms_05.json

And it seems that worked (however I'm not 100% sure which particle_parms_xx.json I should use). No error message. (I'm pasting below the entire in-terminal message). I'm also confused regarding the *99* files I got.

I got as output the following files

refinestats_05.txt

eigval_05.txt

traj_it05eg00.hdf

traj_it05eg01.hdf

class_it05eg00.hdf

particle_parms_99.json

threed_99_even.hdf

threed_99_odd.hdf

fsc_unmasked_99.txt

class_it05eg01.hdf

A few more questions (I hope you don't mind)

traj_it05eg00.hdf and traj_it05eg01.hdf, differ in the number of eigval? Which one did you use to display trajectory in the example of have on e2tomo_more? (In my case traj_it05eg00.hdf exhibits larger movement than traj_it05eg01.hdf)

Is there a good test(rational) to change --nframe (I believe default is 5), --nptcl, or even --nstd.?

In which cases would you recommend to use --replace3d ?

And finally, do the files class_it05egxx.hdf correspond to the 3D volumes before the trajectories are built?

Many thanks,
Maia

e2spt_trajfromrefine.py --path spt_118 --iter 5 --parminit spt_118/particle_parms_05.json

Refine stats saved to spt_118/refinestats_05.txt. The three columns are:

Translation - mean: 0.00 std: 0.00

Rotation - mean: 0.00 std: 0.00

Score - mean: -0.30 std: 0.05

Generating eigen-trajectory...

Eigen values saved to spt_118/eigval_05.txt

Trajectory 0:

Rotation - x: 0.00 y: -0.00 z: -10.23

Translation - x: 0.00 y: 0.00 z: -0.00

Trajectory file written to spt_118/traj_it05eg00.hdf

Trajectory 1:

Rotation - x: -0.00 y: 0.00 z: -1.17

Translation - x: 0.00 y: 0.00 z: 0.00

Trajectory file written to spt_118/traj_it05eg01.hdf

Making averages along trajectories...

[-2. -1. 0. 1. 2.]