"EMAN 2.91 final ( GITHUB: 2021-03-08 11:36 - commit: 81caed2 )
Your Python version is: 3.7.9"
While attempting to extract particles from tomograms, I got an error where the extractptclfromseg.py command was "not found".(command and output mentioned below)
"
$ extractptclfromseg.py Position_15_stack_full_rotx_bin5_preproc__tube_final.hdf Position_15_stack_full_rotx_bin5_preproc.hdf --random 100 --edge 32 --thresh 1.3
$ extractptclfromseg.py: command not found.
"
The functionalities before this step seemed to work well. Not sure why this error shows up? Do I need to install anything additional to run the extraction functionalities?
Best
-Himanshu
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On Sep 7, 2021, at 5:17 AM, Himanshu Sharma <ace.him...@gmail.com> wrote:
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On Sep 10, 2021, at 11:10 AM, Himanshu Sharma <ace.him...@gmail.com> wrote:
Thanks, Steve and Muyuan, and I appreciate the suggestions.@Steve: Yes I remember your older suggestion as I had raised a similar issue before. Given the same reason, I did not want to throw in the error messages without knowing if a protocol for working on imported tomograms already existed. Anyway. I have been working with my tomograms between IMOD and Eman2. For some reason (could be a problem with my data), the reconstruction does not seem to be equally good in EMAN2, hence I had to resort to importing the tomograms.Having said this, I again tried to follow the full pipeline in Eman2 and faced the following errors while trying to find particles from segmentation:command: (I tried varying the box size and massthread but the problem persists)
<Screenshot 2021-09-10 at 17.58.57.png>error:
<Screenshot 2021-09-10 at 17.59.24.png>
the segmentation does not look great at this stage, but as I am just trying to get an initial test model, I did not bother improving this further. I intend to extract parts of the outer membrane as seen here.
<Screenshot 2021-09-10 at 18.02.40.png>
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<Screenshot 2021-09-10 at 18.02.40.png><Screenshot 2021-09-10 at 17.59.24.png><Screenshot 2021-09-10 at 17.58.57.png>
On Sep 13, 2021, at 9:30 AM, Himanshu Sharma <ace.him...@gmail.com> wrote:
Hi,The e2spt_extractfromseg error was seen one more than one tomogram. I have tried this with three tomograms and seem to get this error. I tried to clear all the particles and the error persists. However, there is something I observed after running the command. In spite of the error, the program seems to find some particles (particles_01 in the image) and this (particle identification) does not appear in the program log. Additionally, the identified particles do not seem to be good representatives from the trained model (seem to be random picks at best in high contrast features of the tomogram).
<Screenshot 2021-09-13 at 16.18.18.png>this is a screenshot from the tomgram.json file:
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<Screenshot 2021-09-13 at 16.25.38.png><Screenshot 2021-09-13 at 16.18.18.png>