Ellen Zhong
Ellen Zhong
Downsample with .cs particles as source sometimes reads more particles than parse_pose and parse_ctf
Thanks for reporting. Are you providing a different `.cs` file to `cryodrgn downsample` than the `cryodrgn parse_*` commands?
Downsample with .cs particles as source sometimes reads more particles than parse_pose and parse_ctf
Could you email the `.cs` file to myself ([email protected]) and Vineet Bansal @vineetbansal ([email protected]). We will take a look. Thanks!
Thanks for your question! There are a couple of options for selecting particles from the desired cluster: 1. You can select the particles using the `cryoDRGN_filtering.ipynb` notebook from `cryodrgn analyze`--...
Thanks for the post. Yep, you should run `cryodrgn analyze` first before `cryodrgn analyze_landscape`. I can add a note/check for that. FYI I've been testing out the landscape analysis tool...
Just another usage note for `cryodrgn analyze_landscape` -- you should inspect the automatically generated `mask.mrc` in the output directory and make sure it covers the particle, including the heterogeneous parts...
That's a good suggestion. It should be very straightforward to add an `--ind` flag to `cryodrgn downsample` or `cryodrgn preprocess`.
I added a flag `--ind` to `cryodrgn downsample`. It looks like there is already an `--ind` flag to `cryodrgn preprocess`. You can generate a random 100k selection with the command:...
Ah, I forgot to mention. Since the particle stack is now a subset, you'll have to filter the ctf.pkl and pose.pkl by the selection as well before giving it to...
Great, glad to hear that it worked! Thanks for reporting the AMP warning... good to know about the deprecation date. The latest version of cryoDRGN uses the recommended Pytorch.AMP library,...
Can you share the command that you ran? I'm curious about the architecture settings you used -- thanks!