Babel Plugin, Version 1.12
This plugin reads and displays molecular structure files in several formats using the Babel program to translate them into PDB files which are easily read by VMD. In order to use this plugin Babel 1.6 must be installed on your computer and must be executable in your default command path so that the Babel plugin can run it via calls to system(). Babel 1.6 is available from the OpenEye Babel web site
This table lists all of the molecule file formats that Babel will translate to the PDB format which can be loaded by VMD:
|Alchemy||AMBER PREP||Ball and Stick|
|Biosym .CAR||Boogie||Cacao Cartesian|
|Cambridge CADPAC||CHARMm||Chem3D Cartesian 1|
|Chem3D Cartesian 2||CSD CSSR||CSD FDAT|
|CSD GSTAT||Free Form Fractional||GAMESS Output|
|Gaussian Z-Matrix||Gaussian Output||Hyperchem HIN|
|Mac Molecule||Macromodel||Micro World|
|MM2 Input||MM2 Ouput||MM3|
|Mopac Cartesian||Mopac Internal||Mopac Output|
This plugin is used only to read files. VMD does not currently support writing to these formats.
Babel performs a reasonable translation in most cases, however it is unavoidable that some formats may contain information which doesn't have a corresponding record in PDB files, so this information may be lost in the translation, and thus unavailble when loaded into VMD.
Compressed files will need to be expanded before this plugin can read them.