search

haddocking / pdb-tools

A dependency-free cross-platform swiss army knife for PDB files.
https://haddocking.github.io/pdb-tools/
Apache License 2.0
372 stars 113 forks source link

Add option to pdb_tidy to only add TER between different chains #101

Closed amjjbonvin closed 2 years ago

amjjbonvin commented 3 years ago

By default pdb_tidy adds TER statement for every break, within or between chains.

This might not always be desirable. Between chains is in principle always OK, but within the same chain not. E.g. missing density in X-ray structures result in missing residues, but the gaps do not contain TER statements.

Those additional TER statement might cause third party software to handle those are real termini and add for example charges...

JoaoRodrigues commented 3 years ago

Won't pdb_tidy -strict help? The strict version only adds TERs between chains.

amjjbonvin commented 3 years ago

Must have read over it! :-)

But this should rather be the default since consistent with PDB

joaomcteixeira commented 2 years ago

Note that making -strict the default would require changing pdb-tools to v3 to keep Semantic Versioning 2.0 compatibility because it would imply a huge change in the API -> result flow. Maybe we should tag this issue to v3?