Last Modified

   1 January 2020

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Free HyperChem Add-on Program

Molecular Modeling Tools for HyperChem, Revision C1

Compatible to the Protein Data Bank format versions 3.0-3.3.



Package Contents

Control Center

The "Control Center" can be used for controlling the module programs in Molecular Modeling Tools for HyperChem and performing protein modeling and functional analysis more efficiently, using HyperChem. The program can save the operations together with the used file names and the used module program names.


Interface Selection

In HyperChem, many options such as geometry optimizations can selectively apply to the selected molecules, atoms, and residues, etc. The "Interface Selection" program can be used for effectively performing the protein modeling and functional analysis by these HyperChem options. This program can be used for many purposes such as searching for atoms and residues involved in protein-protein and protein-ligand interactions (interface). The program can make many selection patterns which are not prepared in HyperChem. Additionally, the program can be used for safely deleting structure in the HyperChem workspace. The latest version of this program can automatically treat the partial geometry optimizations for the selected part of the structure.


Geometry Correction

The "Geometry Correction" program can be used for resolving a particular problem under a protein modeling using HyperChem 5.x / 6.x / 7.x. This program can correct the NH bond orientation of the HE proton in arginines, the CH bond orientation of the HG proton in leucines, and the lone pair orientation of the sulfur atom in cysteines and methionines. These problems do not occur in HyperChem8.0.3.


Recommended Minimum System Requirements

Processor: Intel Pentium III, Pentium 4, Celeron, Core2Duo, or Xeon (AMD processor is unidentified)

Operating System: Microsoft Windows 95, 98, NT4, 2000, XP, or Vista

Memory (RAM): 128 MB (256 MB recommended)

Other: Hard Disk; CD-ROM drive; Mouse


Software Requirements

HyperChem*: 5.x/6.x/7.x/8.0x (Windows version; Student edition is unidentified)

TclPro1.2: TclPro1.2 (Windows version) is necessary to run Molecular Modeling Tools for HyperChem. TclPro1.2 is available on the Web free of charge.


Installation Instruction

Installation of TclPro1.2

1. Download the TclPro1.2 installer for Windows from the following URL address to an arbitrary drive.

URL: https://www.tcl.tk/software/tclpro/eval/1.2.html

TclPro1.2 is available from the above Web site free of charge, and its perpetual free license key is also available from the same Web page.

2. Once you have downloaded the TclPro1.2 installer, double-click the icon of the installer. Then, follow the installation instructions provided.


Installation of Molecular Modeling Tools for HyperChem

We assume that HyperChem has been already installed in your computer.

Please do not install HyperChem and Molecular Modeling Tools for HyperChem simultaneously.

You have to have initiated at least once HyperChem program to register your HyperChem environment into Windows Registry.

You must install TclPro1.2 in your Windows system, prior to the installation of this package.

1. Download ModelingTools.zip file to an arbitrary folder.

2. Expand this zip format file to an arbitrary drive or a folder such as C:\Temp folder.

Note that the folder name and the absolute full path name must not contain a space and/or a two-byte font such as Japanese font. For example, you must not expand the zip file to your Windows desktop.

3. Double-click on the expanded Setup icon. For users of Windows95 and 98, the setup wizard can be started by double-clicking on the "Installer.tbc" icon which is found in the same folder, instead of the Setup icon. In these operating systems, you may need to choose the "show all extensions" option of the folder option of Windows.

Follow the installation instructions and click the appropriate selection to agree to the License Agreement of Molecular Modeling Tools for HyperChem.

When the installer requires a license key, you can proceed to the next step using the "Next" button (the installer will display a free license key in default).

After being prompted to proceed through several steps, you will have successfully completed the installation of Molecular Modeling Tools for HyperChem.

If you have used an evaluation version of HyperChem, you must choose the "Evaluation" button within 60 seconds. Otherwise, the program will fail out to connect with HyperChem.

Copy the icons generated on the desktop into the user's folder via the Documents and Settings folder of Windows.


Initiation of Molecular Modeling Tools for HyperChem

1. Double-click on the "MF" icon.

If you have used an evaluation version of HyperChem, you must choose the "Evaluation" button within 60 seconds. Otherwise, the program will fail out to connect with HyperChem.

2. Load a protein molecule system (in an HIN or a PDB format) into the HyperChem workspace using the "New Project" or the "Open" command from the "File" menu of the Control Center program.

3. Initiate the module program from the "Module" menu of the Control Center program.



Both Geometry Correction and Interface Selection module programs become accessible whenever a protein molecule system is loaded into the HyperChem workspace.

A substantial Online-Help (English) is available from individual programs in the package.


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* HyperChem is a registered trademark of Hypercube, Inc.



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