Alexandre Bonvin comments

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                                            Alexandre Bonvin

some i-rmsd values in haddock stats files are not correct

Well - this is not a DeekRand code issue. Not doesn't make sense to open an issue for this here. It's more for us to correct those values before we...

implement Edesolvation energy in deeprank

For this you will need to calculate the atomic solvent accessible area for each atom. And then implement the desolation parameters and combination formula from HADDOCK. Code to be found...

`pdb_tidy` removes the `TER` record between chains and removes last `ENDMDL` in a multi-model PDB

Yes - better too few than too many TER statements. Adding TER statement at any chain break (even within a chain is a dangerous thing since it implies there is...

`pdb_tidy` removes the `TER` record between chains and removes last `ENDMDL` in a multi-model PDB

Any news on this? Is it still relevant or implemented already?

Improve `pdb_merge` to include `TER`s and `END` lines

Yes - but why does it remove the END statements then? Other code don’t do that (e.g. pdb_chain).

Improve `pdb_merge` to include `TER`s and `END` lines

So a simple cat command effectively. Meaning pdb_tidy should always be run to correct things. A very different behaviour than `pdb_mkensemble` for example.

Improve `pdb_merge` to include `TER`s and `END` lines

hmmm…. assumptions… this is asking for troubles… It is this make clear to the users? > Yes. mkensemble has the clear purpose of making a correct ensemble of structures. While...

Improve `pdb_merge` to include `TER`s and `END` lines

How will you explain users that `pdb_merge` does require `pdb_tidy` to make a correct PDB while `pdb_mkensemble` not...

Improve `pdb_merge` to include `TER`s and `END` lines

Probably good indeed

pdb_selaltloc removes residues with (only) alternate locations

This is a serious issue that should be solved.