Parsing lst for original tomogram coordinates

[Jacob Croft]

Hello,

I'm trying to use EMAN2 Jupyter notebooks to read an aliptcls3d_xx.lst file from a refinement and for each particle find the coordinates in the tomogram (with the shift determined by the refinement applied). I don't see the original coordinates in the lst file - do I have to open the particle hdf file to get this information? If so, what is the best way of doing this? Basically I just want to get the transformed coordinates and euler angles for each particle in a lst file. Thanks!

Best,

Jacob Croft

University of Washington

[Steve Ludtke]

Hi Jacob,

there is a program: e2spt_mapptclstotomo.py  which takes refinement results and maps individual particles back to the tomogram for annotation purposes. It's a pretty simple script. Take a look at that and you should see how it's done

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[Jacob Croft]

Thanks for pointing me to that script. I think it makes sense, but for some reason when I am trying to read the .hdf files from jupyter it can't see them, eg:

infile = "spt_188/aliptcls3d_10.lst"

alipm = load_lst_params(infile)
ptcl = []
for p in alipm:
    ptcl.append((p["score"], p["src"], p["idx"], p["xform.align3d"]))

for s,fsp,i,xf in ptcl:

    a=EMData(fsp, i,True)

I get:

Exception: 'particles3d/TS55_particles_bin4.hdf' is not an existing regular file!

I checked the file does exist, and also tried the same lines in a terminal and it was working fine... Is there some way I have to configure Jupyter to be able to read the particles3d/.hdf? Currently I have just used os.chdir() to enter the eman project directory within jupyter, from there is can read the lst files but seemingly not open the particles3d/.hdf files.

Best,

Jake

[Steve Ludtke]

Hmm, not clear exactly what's causing your problem. Changing to the project folder is the correct move. Pretty sure the os.chdir should work, but you could try launching jupyter from the project folder to see if it makes a difference.    However, if your goal is to just get the coordinates in the tomogram, you shouldn't actually need the .hdf file. You already have the information from the .lst file...

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