Csparc2star.py version 0.63 vs older - KeyError: 'rlnAngleTilt'

Troubleshooting
1

Hi @DanielAsarnow

I want to convert use csparc2star.py and star2bild.py to represent particle distribution in 3D.

It worked beautifully on an “older” (sorry can’t find the version number) version of pyem.
Now our IT person installed a new version (0.63) and the procedure doesn’t work at the star2bild.py with the error: KeyError: ‘rlnAngleTilt’

In the “older” version, the particle.star does have the rlnAngleTilt:
data_images

loop_

_rlnImageName #1

_rlnMicrographName #2

_rlnCoordinateX #3

_rlnCoordinateY #4

_rlnAngleRot #5

_rlnAngleTilt #6

_rlnAnglePsi #7

_rlnOriginX #8

_rlnOriginY #9

_rlnVoltage #10

_rlnMagnification #11

_rlnDetectorPixelSize #12

_rlnDefocusU #13

_rlnDefocusV #14

_rlnDefocusAngle #15

_rlnSphericalAberration #16

_rlnPhaseShift #17

_rlnAmplitudeContrast #18

_rlnCtfBfactor #19

_rlnOpticsGroup #20

_rlnRandomSubset #21

_rlnClassNumber #22

But the 0.63 version probably has rlnAnglePsi instead (??): (both input have been generated from the same cryosparc job, just on 2 different machines).
data_images

loop_

_rlnImageName #1

_rlnMicrographName #2

_rlnCoordinateX #3

_rlnCoordinateY #4

_rlnAngleRot #5

_rlnAngleTilt #6

_rlnAnglePsi #7

_rlnOriginX #8

_rlnOriginY #9

_rlnVoltage #10

_rlnMagnification #11

_rlnDetectorPixelSize #12

_rlnDefocusU #13

_rlnDefocusV #14

_rlnDefocusAngle #15

_rlnSphericalAberration #16

_rlnPhaseShift #17

_rlnAmplitudeContrast #18

_rlnCtfBfactor #19

_rlnOpticsGroup #20

_rlnRandomSubset #21

_rlnClassNumber #22

Could you point out if I’m missing a keyword?
Thank you
Vincent

2

Both of your lists of headers have all three angles, which are the only fields necessary for star2bild.py. I’ll need more information about your jobs, commands, and the input files to identify the error.

3

Hi @DanielAsarnow ,

sorry, I made a mistake. As I was detailing my answer, I realized that I had a mixup between 2 cryosparc jobs J56 and J66, that I was running on the 2 machines. I’ve re-ran the 2 versions of pyem on the same job and now it works well.

Sorry again for the misunderstanding.
Vincent