User Guide#
The Read Structure plug-in reads structures from a wide range of molecular file formats.
Files with several structures#
Many formats, such as SDF and extended XYZ files, can hold more than
one structure. By default the step reads all of them. Structures to read
(indices) chooses which: a comma-separated list of indices and ranges
start:stop[:step], counting from 1 with the stop included, e.g. 1 for only the
first structure, or 1:10:2, 20:end.
The first structure read is handled as Structure handling says: by default it overwrites the current configuration. Each later structure is handled as Subsequent structure handling says: by default it goes into a new system and configuration.
The last structure read becomes the current configuration, and the steps that follow work on it. When the step reads more than one structure, its output says which one is now current, e.g.:
The current configuration, which the following steps use, is now structure 2
of 2, C4 H8 O:
System name = 109-92-2_0
Configuration name = C=COCC
Check this line when a file may hold more structures than you expect. If only the
first is wanted, set Structures to read to 1.
Plain XYZ files with several structures#
Plain XYZ files come in several layouts, and the step reads each of them, one after another in the same file:
The standard one: the number of atoms on the first line, a comment (often the name) on the second, then one line per atom. The structures may follow one another directly or be separated by blank lines.
Without the number of atoms: a blank line in its place, or no line at all, then the comment and the atoms. Here a blank line separates the structures.
The Minnesota Solvation Database’s layout: the comment, a blank line, the charge and spin multiplicity, then the atoms, with a blank line between structures. The charge and multiplicity are kept.
Set System name and Configuration name to title to name each structure
after its comment line.