BJWiley23

Yeah I understand the chain Termination but sometimes these TER have an `ATOM` index number and so if you manipulating pdb files let's say like [GenerateUncomplexedProteinPDBFromComplexedPDB](https://github.com/TinkerTools/poltype2/blob/d82f473499335de373ef6e7283c0e9d8135aa5c8/PoltypeModules/pdbxyz.py#L93) for Polytype2 for removing...

Yea I know now that maybe since I was missing hydrogens on 5-FU plus I have crystal structure with 4 chains and 4 molecules of 5-FU that was probably the...

Thanks for sending notes on xml for non-standard residues. I believe it worked

Should `HIS` residues be protonated on `ND1` at the default pH of 7? I thought only this was weird. I don't think it should be and so `HD1` shouldn't be...

Thanks for the resource @jchodera! I would def agree with whatever Schrodinger does 😄. Looks like most of the time at physiological pH it's going to try to make as...

pdbfixer runs with over 10,000 atoms so look like it's just files formatted with over 100,000 atoms. The only thing looks like pdbfixer doesn't like the `H` atom names for...

I realized that Chimera is awful for large systems over 25,000 molecules so I don't even looked at solvated proteins in Chimera any more. I just do it in VMD...

Well I was using the wrong docker 😄. Supposed to be using `us.gcr.io/mccarroll-mocha/bcftools:1.15.1-20220518`. I'm assuming you used `apt-get` to install bcftools in the `r_mocha` docker? If so we know something...

Try this one: ZINC001094026363 `Cc1nnc(CNC[C@@H]2CN(C(=O)[C@@]34CCCC[C@H]3C4)C[C@H]2C)n1C1CC1` Even Zinc doesn't have 3D rdkit molecule for this...

Thanks for all the work you did to check it. Ironically this works on my Mac with `Open Babel 3.1.0` from conda install (`OpenBabel11232220203D`) but with same version on ubuntu...