Timeo is an Olex2 plugin that integrates several symmetry and shape analysis tools into a single graphical interface. Cosmochlore was developed in parallel to Timeo and is designed to run as its background engine.
Formerly Timaeus
Timeo was called Timaeus before version 1.2.0. If you have Timaeus installed, see upgrading from Timaeus.
Features
- Input/output file managing. Every analysis reads atomic coordinates directly from the Olex2 refinement model and produces the necesary I/O files, so there is nothing to write by hand.
- GUI panel. Almost1 every function is available from the Timeo panel under the Tools tab.
- Cosmochlore integration. All the options of Cosmochlore’s commands are reachable through the Cosmochlore tab. See Cosmochlore in Timeo.
- SHAPE 2.1 wrapper. Timeo can write the input files for SHAPE 2.1, run it and parse the results. See autoSHAPE.
- Octahedral distortion parameters. A topology-based reimplementation of the OctaDist algorithm, independent of Cosmochlore’s. See Octahedral Distoriton.
- ηn π-bonded ligands. Timeo can detect π-bonding and can average the donor atoms to the ligand centroid.
- Disorder handling. Disordered parts are measured automatically, and you can choose which parts to combine. See disorder.
Where to start
- Check the requirements and install the plugin.
- Read the usage guide to learn how atoms are selected and how the results are reported.
- Look up individual options in the settings reference.
Pages in this section
| Page | Contents |
|---|---|
| Installation | Requirements, step-by-step setup, troubleshooting and upgrading from Timaeus. |
| Usage | Selecting atoms, π-bonded ligands, disorder handling and output locations. |
| Cosmochlore in Timeo | autoCSHM, autoCSOM, autoODIS and user-defined shapes. |
| autoSHAPE | Running and parsing SHAPE 2.1 from Olex2. |
| Octahedral distortion | Timeo’s own implementation of the OctaDist parameters. |
| Settings | Every phil parameter, with defaults. |
License
Timeo is free software, released under the GNU General Public License v3.0 or (at your option) any later version.
Footnotes
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Functions not available throught the GUI are probably not meant to be used by the common user base. ↩