Import spk error

[ariel234156]

Hi,
I tried to upload particle locations (spk file) to the preproccess step, and I got this error:

`

Traceback (most recent call last): -- 155 | File "/opt/pyp/bin/run/pyp", line 3440, in 156 | tomo_swarm(args.path, args.file, args.debug, args.keep, args.skip) 157 | File "/opt/pyp/src/pyp/utils/timer.py", line 78, in wrapper_timer 158 | return func(*args, **kwargs) 159 | File "/opt/pyp/bin/run/pyp", line 1663, in tomo_swarm 160 | virion_coordinates, spike_coordinates = detect_tomo.detect_and_extract_particles( 161 | File "/opt/pyp/src/pyp/detect/tomo/core.py", line 1290, in detect_and_extract_particles 162 | extract_spk_direct( 163 | File "/opt/pyp/src/pyp/detect/tomo/core.py", line 1355, in extract_spk_direct 164 | spikes = imod.coordinates_from_mod_file("%s.spk" % name) 165 | File "/opt/pyp/src/pyp/inout/utils/pyp_edit_box_files.py", line 26, in coordinates_from_mod_file 166 | subprocess.getoutput( 167 | IndexError: list index out of range `

The coordinates were compatible with the output tomogram (with eight binning), and the file contained three columns [x,y,z] coordinates.
I would be happy to help.
Thank you.

[abartesaghi]

If you are trying to import particle coordinates using .spk files, those must be IMOD model files, not simple text files with coordinates. You have two options, either rename the .txt files to have a .box extension, or preferably, convert your .txt files to IMOD models using IMOD's point2model program. Having the models will allow you to open each tomogram and its corresponding .spk file in IMOD, and confirm that your particles are in the right locations before importing them into nextpyp.

[ariel234156]

Thank you, it's working now.