first, want to say that cisTEM is amazing. My favorite feature is the ab initio 3D. In my opinion it is far better than anything else out there. So THANK YOU!
I wanted to ask whether cisTEM is still under development, and if so are we to expect a GPU accelerated version at any point? Any idea on the timeline for any update to the software?
Lastly, I understand it is possible to run jobs through command line. Is there any documentation available on how to run all job types? In particular I'd like to be able to run 2D classification and to somehow select results in command line as well (possibly by opening the image on my local machine but designating in command line which classes to keep). Is this possible? if so how?
many thanks again!
Yes cisTEM is still be developed, and we hope to release a new version soon. GPU acceleration is a possible addition, but at the moment it is not high on the priority list as we feel cisTEM runs quite fast on cpus.
It is possible to run the programs from the command line They exist as binaries in the cisTEM directory, so for example to run 2D classification you can run the refine2d program. This will output a text file that will contain the best class for each image, so you can parse this file to do sorting. However, you will likely need to wrap the program into scripts if you want to use parallelization, which is something that others have done, but I don't have any documentation for - I am more than happy to help you though.
Also, Improving command line access is something that we are keen to work on in the near future, so I hope this will be improved soon.