BJWiley23

For R as well too.

Just read down further. Nevermind :+1: Thus, we turn on the --output-genome-bam option in the fifth line. Note that this option is only available when you build references from a...

Just ran `obabel -ipdb -opdb output.pdb -O output.connected.pdb` so the protein atoms are connected and still get same issue. I would def say this is now a bug.

OK I see what is happening now after trying to run `obabel -ipdb -opdb output.pdb -O output.connected.pdb`. It's making a bond from `O3` atom number 5239 to atoms 2602, 2604,...

OK I made the fix to the double bond on the carbonyl and now when I read in the pdb file and write straight to pdb or just plain obabel...

Sorry this is version 3.1.1. The binary version and obabel.__version__ are not updated from conda-forge package.

OK this is now almost getting comical. Take input PDB file straight from RCSB for [4gq6](https://www.rcsb.org/structure/4gq6) and run: ``` obabel -ipdb -opdb -O 4gq6.out.pdb 4gq6.pdb ``` And it converts an...

@ghutchis can we get someone to work on the CONECT issue for PDBs described above. Without this working I don't see PDB functionality being stable at all.

So is this an issue with the PDB file? Also not sure what you mean with "in addition to change the assigned A 110 into A 131". Does this mean...

RDkit might be better but the message I am now trying to confer isn't about the bonding. I am not too worried about the bonding information either. Let's table the...