CUBY logo
back to Tools


This script provides multiple functions working on a geometry file. They are selected by a commandline option. If the output of the action is a geometry, it is printed to standard output by default, in the same format as the input geometry. This can be modified by the option -o (--output) that redirects the output to a file. If file format can be determined from name of the output file, it is used, otherwise the format of the input file is used.

Get selection

Option -s or --selection

Prints part of the geometry selected by selection expression (see Atom selection expressions) to standard output. The geometry is printed in the same format as was the input geometry (xyz or pdb).

Example: Following command will select all atoms but hydrogens from file

geometry -s "@~H"

Get selection list

Option -S or --selection-list

Prints list of atom indexes (starting at 1) selected by selection expression (see Atom selection expressions).

Example: Following command will print list of all hydrogens and oxygens in file

geometry -S "@H,O"

Explode residues

Option -e or --explode [factor]

Moves each residue away from system center of mass by given factor (new distance = old distance * factor). This function was added just to produce animation of molecule broken into pieces.

Randomize coordinates

Option -r or --randomize [amplitude]

Add random numbers with selected max. amplitude to coordinates.

Apart from just making noise, there are two useful applications:

Root mean square deviation (RMSD) of coordinates

Option -d or --rmsd

Move the second geometry file to minimize its RMSD with the first one.

Prints the RMSD value in Å, distances between atoms and the fitted geometry