Read Molecule

Description

Read a molecule structure.

Input Ports

None

Parameters

file format list Select the format of the sequence to be read. The available formats are:
Plain Coordinates
The PlainCoord option is to process a simple file of X-Y-Z coordinates with the atom type designated by the entry in the periodic table. This format is nearly identical to the DmolXYZ file format.
Plain Coordinates plus displacement
Same as before plus a displacement vector for each atom: it is available as the offset_lst field in the molecule data structure and is used by a special visualization technique (not available in STM3) to show atom vibration around its equilibrium position.
Gaussian Cube
Output format of Gaussian. Only the atomic structure is extracted, not the electron density data. This format contains unit cell information.
PDB
Protein Data Bank format. This format contains unit cell and symmetry information.
GAMESS xyz Cube
GAMESS Plotting Option .F33 file output.
GAMESS xyz (from Perl extractor)
Read in GAMESS xyz format from the PERL extraction.
DCAR
Read a MSI DMOL DCAR file.
DMOL XYZ
Read a MSI DMOL COORD file.
CONVEX Mopac ESP
Mopac Electrostatic Potential.
Mopac XYZ
Mopac coordinates.
TRIPOS MOL2
Read a TRIPOS MOL2 file.
MOL
Read a MOL file.
CHEM-3D
CHEM-3D file.
MM3
Molecular Mechanics Code MM3.
SHEL-X
SHELX is a set of programs for crystal structure determination from single-crystal diffraction data. It is also the format used by the Inorganic Crystal Structure Database. This format contains unit cell and symmetry information.
Units list Measurement units used in the files. Currently the only format that uses Bohrs is the Gaussian Cube.
File name file browser The file name to be read.
Hydrogens toggle Enable Hydrogen atoms reading.
H bonds toggle Enable computation of H bonds.
Force Bonds Recomputation toggle Force bonds recomputation even if bonds definitions are already present in the file
Freeze bonds toggle Don't recompute bonds.
Bonding Range Adjustment slider Percentage of variation of the maximum distance between atoms to form a bond.
H Bonding Range Adjustment slider Percentage of variation of the maximum distance between H and an atom to form a bond.
H Bond Max Distance slider Maximum lenght of an H bond.
H Bond Max Angle slider Maximum angle HXY (in X__H..Y where .. is the H bond) to form an H bond.

Output Ports

molecule MolecularDataType Molecular data.

See also