Patches/9v3

Patches on this page can be applied to Modeller 9v3 to fix some minor problems. (Use the Unix `patch` command, or apply them by hand.)

(!) The patches are listed in chronological order (oldest first), so you should apply them in this order to avoid problems.

• append_model.patch: make alignment.append_model() copy the model's resolution, R-factor, name and source to the alignment.
• structure-residue.patch: give residue objects in template structures all of the properties of alignment sequence residues (e.g. query of gaps) as well as most of those of model residues (xyz coordinates, etc.)
• reread-ini-model.patch: make sure that `automodel` can read its initial model (`.ini` file) back in correctly in cases where this file contains HETATMs, waters, or hydrogen atoms, and you do not have the corresponding flags (`env.io.hetatm` etc.) set.