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EMAN1 to FREALIGN conversion #1985

Open leginonbot opened 8 months ago

leginonbot commented 8 months ago

Author Name: Michael Cianfrocco (@mcianfrocco) Original Redmine Issue: 1985, https://emg.nysbc.org/redmine/issues/1985 Original Date: 2012-08-08

Gabe tells me that there is a routine within Appion for converting EMAN1 euler angles & particles into FREALIGN format. Can someone point me to the script? I can convert almost all data types into FREALIGN/FreeHand format except EMAN1.

Thanks, mike

leginonbot commented 8 months ago

Original Redmine Comment Author Name: Anchi Cheng (@anchi2c) Original Date: 2012-08-14T03:08:14Z

You need to do it in two steps using

appionlib.apEulerCalc.EulersToRotationMatrixEMAN appionlib.apEulerCalc.rotationMatrixToEuler3DEM

This assumes, I think, that eman uses top-left origin data and 3DEM (same as SPIDER without mirror and Frealign) uses lower-left origin data. It may need confirmation because I'ven't done enough recently.

Also be careful if you are dealing with icosahedral symmetry because EMAN1 532 convention does not work in Frealign.

For converting EMAN Imagic Stack to MRC with the data flipping, use

pyami.imagic2mrc.imagic_to_mrc with yflip=True.

Follow Issue #1873