Patches/9v3: Difference between revisions
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Patches on this page can be applied to Modeller 9v3 to fix some minor problems. (Use the Unix | Patches on this page can be applied to Modeller 9v3 to fix some minor problems. (Use the Unix <code>patch</code> 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. | |||
* [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 | * [http://salilab.org/modeller/archive/patch-9v3/reread-ini-model.patch reread-ini-model.patch]: make sure that <code>automodel</code> can read its initial model (<code>.ini</code> file) back in correctly in cases where this file contains HETATMs, waters, or hydrogen atoms, and you do not have the corresponding flags (<code>env.io.hetatm</code> etc.) set. | ||
[[Category:Patches]] | |||
Revision as of 20:56, 16 August 2022
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
automodelcan read its initial model (.inifile) back in correctly in cases where this file contains HETATMs, waters, or hydrogen atoms, and you do not have the corresponding flags (env.io.hetatmetc.) set.