Hello, my name is Hyelim Jang, and I am a master's student at Yonsei University in South Korea.
I am currently performing subtomogram averaging using RELION, but I am encountering an issue with the pick tomogram step. There are too many reconstructed tomograms, and it is difficult to accurately pick only the ribosomes, so I decided to use the template matching method. I have used an already known cryo-EM 3D map (.mrc) file as the template. I have installed STOPGAP in a MATLAB MCR environment and have been working with it.
The preparation of the files is almost complete. I have an angle list file (.mat format), a wedge list file (.star format, created separately for each tomogram as the angles vary), a template file (.mrc format), and a reconstructed tomogram file (.mrc, generated from RELION). I used "stopgap_tm_parser.sh" to create the tm_param.star file and believe I have correctly adjusted the paths for my environment.
Now, I am trying to run STOPGAP using the "run_stopgap.sh" script, but after running it, I only see the "Running" message, and when I check the CPU usage, no related commands appear. Before running the script, I have modified all the paths for the connected scripts to match my environment, but I am unsure why this issue is happening. If everything is running correctly, could you tell me what command should appear in the CPU usage? Also, if there is any additional information I should provide, please let me know. (All work has been conducted in a local environment.)
Thank you for providing such an excellent program at no cost.
Hello, my name is Hyelim Jang, and I am a master's student at Yonsei University in South Korea.
I am currently performing subtomogram averaging using RELION, but I am encountering an issue with the pick tomogram step. There are too many reconstructed tomograms, and it is difficult to accurately pick only the ribosomes, so I decided to use the template matching method. I have used an already known cryo-EM 3D map (.mrc) file as the template. I have installed STOPGAP in a MATLAB MCR environment and have been working with it.
The preparation of the files is almost complete. I have an angle list file (.mat format), a wedge list file (.star format, created separately for each tomogram as the angles vary), a template file (.mrc format), and a reconstructed tomogram file (.mrc, generated from RELION). I used "stopgap_tm_parser.sh" to create the tm_param.star file and believe I have correctly adjusted the paths for my environment.
Now, I am trying to run STOPGAP using the "run_stopgap.sh" script, but after running it, I only see the "Running" message, and when I check the CPU usage, no related commands appear. Before running the script, I have modified all the paths for the connected scripts to match my environment, but I am unsure why this issue is happening. If everything is running correctly, could you tell me what command should appear in the CPU usage? Also, if there is any additional information I should provide, please let me know. (All work has been conducted in a local environment.)
Thank you for providing such an excellent program at no cost.