Please note, while you are able to optimize the entire scene, most force fields are not parameterized for multiple discrete molecular structures, and you will be relying on the through-space forces defined in the force field (mainly van der Waals and electrostatic), if defined at all. To do this, you can change the optimization scope to optimize the entire scene. However, you may wish to optimize several discrete molecular structures at the same time and in relation to each other. ChemDoodle 3D therefore will optimize molecular structures separately and individually as you are editing them. Most small molecule force fields are optimized for describing individual discrete molecular structures. ChemDoodle 3D now allows full scene modeling simulations.Major new features include the ability to perform full scene modeling simulations, an implementation of the FIRE optimizer, 3D molecular structure alignment, improved bond deduction with new bond order perception algorithms, and more. Linux KDE URL launches are not functional with Java, so we included a workaround to launch URLs when running ChemDoodle 3D on Linux with KDE.ĬhemDoodle 3D v6.6 is a feature update to ChemDoodle 3D.Corrected an issue for CIF files to adjust the fractional coordinates of unit cell atom definitions to be within the unit cell if not (not the transformed fractional atoms, but the original input).Then restart the ChemDoodle 3D application. Do this by going into Preferences for the ChemDoodle 3D application, selecting the Files tab, and then unchecking “Use Native Filechooser” in the Filechooser settings. But in ChemDoodle 2D and 3D, you may switch to the non-native file chooser which will not be affected if you wish to use such accessibility software and ChemDoodle 3D at the same time.
There will still be an issue with the file chooser, as that is a compatibility issue on the Java side that we cannot control. This update stops the hanging and allows the software to continue to function. Some users experienced application hanging on macOS when accessibility features or 3rd party applications using macOS accessibility APIs are enabled.Improved torsion and inversion force calculations for more efficient modeling.This update is recommended for all users. ChemDoodle 3D v6.6.1 is a maintenance update fixing a handful of issues.
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