Visualization and Manipulation of Molecules with HyperChem

Building, Visualizing and Manipulating Molecules

HyperChem is an integrated desktop molecular modeling system. Its building, visualization and manipulation capabilities are linked to its extensive computational features. In addition to helping you better visualize 3D molecular structures, HyperChem lets you easily set up, perform and interpret results from a wide variety of simulations and computations, including geometry optimizations and molecular dynamics runs.

Building Molecules

HyperChem uses a simple sketch-and-build method for building molecules on the screen and offers several means of creating and modifying 3D molecular structures.

Model Builder

Converts a 2D sketch into a 3D structure.
Defines stereochemistry before or after model building.
Adds hydrogen atoms automatically.
Sets bond lengths and bond angles to appropriate values.
Uses sophisticated algorithms to set rings and cages to appropriate structures.

Tools for peptides and nucleic acids

Using HyperChem, you can easily select residues and specify secondary structures from a menu.

Tools for modifying molecules

Substitute an atom or change bond order with a mouse click.
Mutate amino acid or nucleotide residues.
Translate, rotate, reflect or invert all or part of a molecule.

Files

Read and write files in HyperChem INput (HIN), Brookhaven Protein Databank (PDB), Isis Sketch (SKC), MDL (MOL), OPAC Z-matrix and Tripos (MOL2) formats.

Visualizing Structures

Molecules can be rendered on the screen in several modes: sticks (stereo optional), dot surfaces, disks, or space-filling shaded spheres. HyperChem includes an array of visualization and manipulation tools to help you better understand molecular structures. You can:

Highlight, color, or hide parts of a molecular system.
Display peptide structure using ribbons.
Color a DNA backbone one color throughout.
Color a substrate differently from an enzyme.
Highlight a particular ring in a complicated molecule.
Optionally display hydrogens.
View slices of molecules.
Display computational results.
Animate vibrational modes of molecules.

Consistency Gives Ease of Use

The HyperChem user interface consistently employs a select-and-operate method to simplify use. Simply select a set of atoms, residues or molecules with the mouse and then apply the desired operation or tool.

Making and naming selections

Selecting atoms, residues, or molecules is easy. You can select a particular ring, a specific side chain, a peptide or nucleic acid backbone, all atoms within a radius of a central atom, the shortest path between two atoms, or combine all these possibilities.

Once you have made a selection, you can "name" it for future use. Named selections are stored in HIN files and can be restored by picking the name from a menu.

Selections and Visualization

Selections can be used to control the display. You can:

Color a selection to distinguish it from the rest of a molecule.
Hide a selection from view, or hide the rest of the system, to focus on a region of particular interest.
Label a selection by element, type, chirality, residue name or charge.

Selections and Manipulations

You can apply an array of manipulation tools to selections to give complete control over molecule building. You can:

Rotate and translate a selected molecule or part of a molecule apart from the rest of the system.
Adjust selected bond lengths, bond angles and torsion angles.
Select a side chain in a molecule and rotate it about the connecting bond.
Invert and reflect selections, controlling stereochemistry and conformation.
Delete a selection, or copy and paste it using the clipboard.

Selections and Measurement

Selections provide a quick way to get at structural information. The atoms do not need to be bonded, so through-space measurements are easily made.

Selecting a single atom reports the type and position of that atom.
Selecting two atoms reports the distance between them.
Selecting three atoms reports the angle connecting them.
Selecting four atoms reports the dihedral angle.

Selections and Calculations

Selections enable restraints to be placed on molecular mechanics calculations, parts of molecules to be held frozen, and structural features to be tracked through dynamics runs.

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