Department of Natural Sciences The Hebrew University of Jerusalem The Open University of Israel Shoham - The Center for Technology in Distance Education home page Continuous Symmetry Measures

CoSyM Calculators - Technical Help

The CoSyM Calculators page provides an online interface for the calculations of the following symmetry measures: the continuous chirality measure (CCM), the basic symmetry measure (CSM) and the continuous shape measure (CShM). Click here for theoretical background on the different symmetry measures. A CoSyM tutorial is available here.

This page includes a Jmol window for viewing molecules in three-dimensions. Click here for technical help regarding the Jmol window.

To start a calculation, the molecule should be in pdb format (click here for specification of the pdb format). If the molecule has many hydrogen atoms, it is recommended to delete them before making the calculations in order to speed up the calculation. See links to relevant online programs.

1. CoSyM Screen
2. Uploading a molecule
3. Defining the calculation
4. Calculating the continuous chirality measure - CCM
5. Calculating the basic symmetry measure - CSM
6. Calculating the continuous shape measure - CShM
7. Calculating the distance from a specific point group

1. CoSyM Screen
The CoSyM Calculators screen is divided into four areas: the upload molecule area, the Jmol window to view the molecule in 3D, the calculation area to define the calculation type and view the results, and a history window to follow the input and output data. See screenshot below. The calculation area and history window appear only after a molecule is loaded.

Screenshot of the CoSyM calculators page

2. Uploading a molecule
To upload a molecule, click the browse button on the top left side of the screen, and choose the file from your personal computer. Please note that the file must be in pdb format. Click on "Display File" and wait for the molecule to appear in the Jmol window (click here for Jmol help). Note that the name of the file appears above the Jmol window. In addition, calculation type buttons appear at the top right of the screen (see below).

Calculation type buttons

3. Defining the calculation
The calculation area includes four options, but only three are currently active. Click the relevant button for the desired calculation. For each calculation, a different menu appears in the area below the calculation type buttons. The input and output data is shown in the history window at the bottom right of the screen.

4. Calculating the continuous chirality measure
The chirality calculation answers the question "how chiral is a molecule?" or "how far a molecule is from an achiral structure?" Press the chirality button and then press "Run chirality calculation". Wait for the result to appear under the title "Result" above the history window, or click "cancel" to stop the calculation. It is recommended to copy the result to a piece of paper before going on to the next calculation.

Please note: as part of the calculation, the original structure is normalized, so that after the calculation, the original structure and the computed structure are on the same scale. The molecule presented in the Jmol window after the calculation is the original normalized structure and appears smaller than the original molecule. The normalized molecule can still be used for other calculations, though the bond lengths of the normalized structure are chemically meaningless. To reload the original structure click "Display File". Note that the data in the history window is deleted.

5. Calculating the basic symmetry measure
Calculation of the distance from basic symmetry elements, C2 or σ , can be performed by clicking the "symmetry elements" button. Under the calculation type buttons, new buttons appear for each symmetry element:

Please note that the i button is not currently active. Choose the relevant element button, click "Next" and then click "Run Calculation". Wait for the result to appear under the word "Result" above the history window, or click "cancel" to stop the calculation. It is recommended to copy the result to a piece of paper before going on to the next calculation.

Please note: as part of the calculation, the original structure is normalized, so that after the calculation the original structure and the computed structure are on the same scale. The molecule presented in the Jmol window after the calculation is the original normalized structure and appears smaller than the original molecule. The normalized molecule can still be used for other calculations, though the bond lengths of the normalized structure are chemically meaningless. To reload the original structure click "Display File". Note that the data in the history window is deleted.

Graphical representation of the results
The calculated model - the geometrical structure with the desired symmetry that is the closest to the original molecule - can be displayed in the Jmol window using the buttons that appear below the Jmol window:

1. - Displays the original normalized structure.
2. - Displays the calculated normalized structure.
3. - Starts animation that toggles between the original and calculated structures.
4. - Stops the animation.

Use the Jmol menu to save the calculated structure file (click here for Jmol help). Two models appear in the saved file. Model 1 is the original structure and model 2 is the calculated structure. To keep the calculated structure only, edit the file using a simple text editor (e.g., Notepad) and delete the data of the first model. Note that this structure is chemically meaningless.

6. Calculating the continuous shape measure
The continuous shape measure allows the estimation of the distance of a molecular structure from a specific polyhedron, e.g., tetrahedron, square, triangular prism, octahedron, and more.The calculation ignores the chemical differences between the atoms end treats them as geometrical points in space. To start the calculation, click the "shape" button. A question appears: "Does the molecule have a central atom?" - Click yes or no according to the molecule in question. In the next stage, choose the number of vertices in the structure (without the central atom). Click on the correct number.

Once the number of vertices is defined, the specific polyhedron should be chosen. For example, for a six vertices shape, the following geometrical shapes appear:

Choose the relevant shape - the octahedron or any of the triangular prisms. Note that the name of each polyhedron appears as a tool tip upon pointing the mouse at the specific shape. In the last stage, users are asked to review the history window to make sure all parameters are correct. Choices made can be changed by clicking on the "Back" button. Click "Next" to continue and then click "Run Calculation". Wait for the result to appear under the title "Result" above the history window, or click "cancel" to stop the calculation. It is recommended to copy the result to a piece of paper before going on to the next calculation.

Please note: as part of the calculation, the original structure is normalized, so that after the calculation the original structure and the computed structure are on the same scale. The molecule presented in the Jmol window after the calculation is the original normalized structure and appears smaller than the original molecule. The normalized molecule can still be used for other calculations, though the bond lengths of the normalized structure are chemically meaningless. To reload the original structure, click "Display File". Note that the data in the history window is deleted.

7. Calculating the distance from a specific point group
The point group button is not currently active. However, calculating the distance of a molecule from a specific point group is possible through other types of calculations:

  1. The distance from groups C2 and Cs can be calculated using the basic symmetry measure.
  2. The distance from a polyhedral point group can be calculated using the continuous shape measure of specific polyhedrons: planar square (D4h), tetrahedron (Td), octahedron (Oh) and more. Note that this calculation ignores the chemical differences between the atoms.




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