How to convert .hdf file to star file again?

[d sun]

I am dealing with a cryo-EM dataset. I first did auto-boxing by Relion. Then, I used sxrelion2sprax.py to convert my .star to .hdf. After Kmeans-2D classification by Sparx, I would like to convert .hdf back to .star. Could you please tell me how to convert .hdf to .star again? Thanks!

[Steve Ludtke]

star files are text files, not image files. You can convert HDF files to MRC stack files by saying

e2proc2d.py file.hdf file.mrcs

not sure if this will encompass everything you are trying to accomplish...

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On Jul 7, 2016, at 3:33 PM, d sun <dwsu...@gmail.com> wrote:

I am dealing with a cryo-EM dataset. I first did auto-boxing by Relion. Then, I used sxrelion2sprax.py to convert my .star to .hdf. After Kmeans-2D classification by Sparx, I would like to convert .hdf back to .star. Could you please tell me how to convert .hdf to .star again? Thanks!

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[Mike Strauss]

Hi Sun

hdf files contain everything you need, if the headers are properly populated.  You can write a python script that will take the header information from the hdf and output it to a text file.  You can use relion_star_loopheader to help get the star file started, but you have to know what parameters you want to populate it with (ctf, source image, position information, alignment parameters, etc..).  From there, you just need to make an mrc stack as Steve mentioned.

Regards,

mike

[d sun]

Hi Mike,

Basically, I first converted my .star to .hdf by sxreliontospax,py.  It generated: Coordinates (contains all my .box in my .star), sparx_params_ctf.txt (ctf information for my particles). After Kmeans-2D classification,  I split  multi_ref.hdf into single hdf file. After combing the good class of single hdf file into another combined hdf file, I would like to convert the new combined .hdf to .star for Relion-3D refinement. I can use sxheader.py to import my ctf to the new combined .hdf file. But then, can you give me a example of pyhon scrip about how to convert .hdf to a text file?

Thanks!

[Paul Penczek]

Zhong Huang can help

Regards,

Pawel

[Mike Strauss]

Hi,

I'm afraid don't have a python script available at this point. But you
can look at the sparx wiki on how to look at the header information of
hdf files. That should get you started.

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