Patches: Difference between revisions
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* [http://salilab.org/modeller/archive/patch-9v3/append_model.patch append_model.patch]: make alignment.append_model() copy the model's resolution, R-factor, name and source to the alignment. | * [http://salilab.org/modeller/archive/patch-9v3/append_model.patch append_model.patch]: make alignment.append_model() copy the model's resolution, R-factor, name and source to the alignment. | ||
* [http://salilab.org/modeller/archive/patch-9v3/structure-residue.patch 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.) | * [http://salilab.org/modeller/archive/patch-9v3/structure-residue.patch 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.) | ||
* [http://salilab.org/modeller/archive/patch-9v3/reread-ini-model.patch 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. | |||
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Patches for old versions: ["/9v2"] ["/9v1"] ["/8v2"] ["/8v1"] | Patches for old versions: ["/9v2"] ["/9v1"] ["/8v2"] ["/8v1"] | ||
Revision as of 18:10, 13 March 2008
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.
Patches for old versions: ["/9v2"] ["/9v1"] ["/8v2"] ["/8v1"]