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generatebio / chroma

A generative model for programmable protein design
Apache License 2.0
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Trajectory cif file won't open in ChimeraX #4

Closed Guillawme closed 7 months ago

Guillawme commented 7 months ago

Hello,

This is so cool! I just tried playing with the demo colab notebook and ran the "get a protein" example with the default 160 residues, and downloaded the trajectory cif file. I can open it in PyMOL and play the trajectory. But when trying to open it in ChimeraX (a viewer I am more familiar with), I get this error:

Summary of feedback from opening /home/guillaume/Downloads/protein_trajectory.cif
warnings    Skipping atom_site category: Missing column 'type_symbol' near line 231
No mmCIF models found.

Attaching this particular protein_trajectory.cif.txt file just in case it is helpful, but I suspect this would happen with any file, just with the error at a different line (I had to add a .txt extension for GitHub to accept uploading, you will need to rename it and remove this extension).

Guillawme commented 7 months ago

I get the exact same error when trying to open the corresponding protein.cif.txt file with ChimeraX. Also opens fine in PyMOL.

agarrubio commented 7 months ago

I have the same problem. I had to convert that 'cif' to 'pdb': https://mmcif.pdbj.org/converter/index.php?l=en

There is also this software, which I haven't tried: https://github.com/PDB-REDO/cif-tools

wujiewang commented 7 months ago

We don't use ChimeraX, so we are not aware of the problem. We will try to look into it.

For the generated Protein Object, you can also dump to pdb directly with .to_PDB() if that is easier.

wujiewang commented 7 months ago

@Guillawme @agarrubio

hey, @ggrigoryanv fixed the write_CIF functions by adding atom elemnt types with 2f3f32a0814821fdcff723088b699b94c1b374b0. I tested it and it works. You can get the change by installing from github.

Thanks so much for the feedback.