Filament tracer coordinates

[Andrea Dallapé]

Hello,

I have a dataset of tomograms reconstructed with IMOD (and I cannot reconstruct the tomograms from the tilt series at the moment, sorry).

I find filament tracer in Eman2 particularly user-friendly and fast for some filaments I want to obtain a structure. Even if the tomograms were not reconstructed in Eman2, I'm able to use e2tomo_drawcurve.py tomograms.mrc to trace the filament of interest.

Now, I'm aware I cannot extract in Eman2 because I don't have the tilt series, but I would like to ask you if there is a method to convert/use the coordinates.

I saw that the tool e2spt_extractcurve.py exists and I'm able to obtain the hdf file (checking in e2display.py or Chimera makes no sense though). Does this method work/make sense?

Eventually, is there the possibility to use e2spt_mapptclstotomo.py using the curve ID and not a refinement? In this way maybe I could get the coordinates using Artiax...

Or do you have any other suggestions?

Thank you so much for your help.

Best,

Andrea

EMAN 2.99.66 ( GITHUB: 2025-04-29 15:00 - commit: c0fb0292f )
Your EMAN2 is running on: Linux-6.8.0-60-generic-x86_64-with-glibc2.35 6.8.0-60-generic
Your Python version is: 3.9.15

[Muyuan Chen]

I think there is a SavePDB button from the GUI that should save a PDB file of the coordinates. I use it to overlay with the tomogram in chimera. You will need to set pixel size of tomogram to 1, because PDB format does not support large numbers.

If you just want the raw coordinates, they are stored as a list of points under the "curves" key in the corresponding json files of the tomograms. It may take some programing to convert to format readable for other software though. 

Muyuan

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[Andrea Dallapé]

mmm ok, this is interesting. I saw the savePDB, but I didn't change the voxel size so things were off.

Ok, I will try it!

Thank you so much!

Andrea

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[Andrea Dallapé]

Hi,

I'm working on converting the pdb obtained by Eman2 filament tracer. One thing I noticed is that I can create maximum 6 IDs (0-5) per tomogram in filament tracer.

Is there a way to increase the number of filaments I can trace in one single tomogram?

Thank you so much,

Andrea

[Muyuan Chen]

Oh, the IDs are for the types of filaments. i.e. ID=0 for microtubule and ID=1 for actin etc. So in the normal workflow if you extract particles with curve id=1 it will extract actin from all tomograms. 

For multiple curves of the same type of protein, just hold Ctrl and click on the micrograph. I think it will create a new curve. And holding Ctrl and clicking on existing points will switch back to that curve so you can add more points to it. 

Let me know if it still works properly. I havent used that for a while.

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[Andrea Dallapé]

Oh yes, it works!

I was not aware of this, thank you so much!

Andrea

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