Ability to choose between PDB sources.

primaryodors / primarydock

PrimaryOdors.org molecular docker.

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Ability to choose between PDB sources. #188

Closed electronicsbyjulie closed 1 year ago

electronicsbyjulie commented 1 year ago

This PR includes:

Ability to choose AlphaFold or ZhangLab as sources for receptor PDBs;
Default receptor PDBs are now from AlphaFold;
Ability to hydrogenate PDBs in the editor;
Complete information about OR9G9;
Viewer is able to read PDBs from RCSB and display ligands.

electronicsbyjulie commented 1 year ago

🟩🟩🟥

Looking into why d-limonene is failing in OR1A1...

electronicsbyjulie commented 1 year ago

Isoleucine is having a similar problem to what threonine was doing; the hydrogens on the delta carbon are not bonding to the carbon, causing them to get left behind when the side chain flexes.

The 1A1 test actually intermittently works, despite the Ile bug. 🟩🟩🟨

electronicsbyjulie commented 1 year ago

🟩🟩🟩

Note that the AlphaFold version of OR1A1 does not have the Asp111 - His243 salt bridge, so this part of the test doesn't apply.