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Hi there!
I'm currently using ampal in a project. I need to download several PDBs to handle with ampal. I looked at the `load_pdb` function in `pdb_parser`, and was thinking about passing an optio…
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Speaking personally, the best outcome of this would be to find that someone has already solved the problems we're thinking about, or at least at least has a solution that can be extended to cover this…
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## Expected Behavior
output PDB files are compatible with other downstream software
## Current Behavior
PDB files are not compatible with e.g. Alphafill (https://alphafill.eu/). The PDB files curre…
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hey quarto is there any way to render Mol* with different type 3D representation for example gaussian surface as default not as cartoon. in your given code viewer.loadStructureFromUrl("./www/traj.xyz"…
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I'm not seeing how one would integrate this mmtf-java package into a working Java program such as Jmol. It has a very large set of dependencies, including
org.msgpack.jackson.dataformat
fasterxml.ja…
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I'm trying to upgrade the [panel-chemistry](https://github.com/awesome-panel/panel-chemistry) Python package to work with [Panel](https://panel.holoviz.org/) 1.x/ [Bokeh](https://bokeh.org/) 3.x. This…
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For some use cases longer chain names/Ids are required, e.g., to encode the symmetry operator when creating biological assemblies.
It would be best if the chain names/Ids can have a flexible lengt…
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I think we should enable, for all the users who do not want to interact with the standard python datastructures, the possibility to interact with the information read in through our software, but dire…
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I've been trying to set up Openfold to test it out this week. It's been somewhat of a struggle but I am sooo close right now.
Everything is installed and no errors along the way.
But now this, .…
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From:
https://covid19.bioreproducibility.org/
Some key pieces would be:
- structure determination method (homology models would be from different source)
- species
- major ligand
- structural …