Minhuan Li

Hi, I want to do a quick follow up on this issue. Why don't we make `PDBFixer` a PyPI package alone? The main OpenMM module seems tricky because of the...

I am not sure if I take it correctly. Do you mean PDBFixer itself can be installed by conda? I didn't see that in the installation tutorials

One common case for me is that, I have installed OpenMM according to the official document: ``` conda install -c conda-forge openmm cudatoolkit=xx.x ``` Then I realize that I also...

Got it! That makes much more sense now. Yes, should add this to the README. Thank you for the clarification.

Hey Jack, I am wondering what is the current situation of the issue (Maybe this is not an issue anymore)? If I have one-column anomalous data (similar to that after...

If I understand correctly, say I have a stacked one-column anomalous data, the only difference would be I have to skip the [line](https://github.com/rs-station/reciprocalspaceship/blob/98409cc8552d22d03d6100c6c1dd01cc369e9647/reciprocalspaceship/dataset.py#L1498)` p1 = p1.expand_anomalous()` in `to_reciprocal_grid` function?

Yes, that makes sense. How about taking another argument like `anomalous=False`? And when set to True, whether to call`stack_anomalous` or skip that line can be determined by the number of...

Thanks for the reply. Yeah, I see what you mean. Actually the pdb file was written out with `gemmi`. I wrote my own [util function](https://github.com/Hekstra-Lab/SFcalculator_torch/blob/1e1e5f32b6898218475d81344ace8e11f7140414/SFC_Torch/io.py#L62) to convert arrays into a...

Yes, the protein structure was predicted using AlphaFold, but we implemented some hacky procedures during its forward pass to guide the prediction. Given the widespread experimentation with AlphaFold methodologies, it's...