Index

3. Description of the Input

5. Bug reports and user feedback

4. Description of the Output

S.C.A.R can give two types of output: the Graphical and Text output, depending on whether the Chemscape Chime plugin has been installed in the user's PC or not.

4.1 Graphics Mode

The Output of the program can be given in graphics mode. It is necessary to download and install the plugin Chemscape Chime version 2.0.2 develloped by MDL. The distribution package can be found at this URL: http://www.mdli.com/download/chime. The screen of the graphical output is divided in two parts. In the Left part of the screen the user can find the Control Panel. The Control Panel constists of four general Control-Links that lead to four groups of commands:

• Configuration Panel
• Calculations Panel
• Rotations Panel
• Aminoacid Groups Panel

In the right part of the screen there is the area of the plugin and the Report Bar a small text field the in which the plugin can give information about the atoms, the residues and the chains selected and the distance between two atoms, the angles and the torsion angles as well.

4.1.1 Configuration Panel

1. Stereo Display

Activates the Stereo Mode.

2. Hydrogen Bonds

Displays the Hydrogen Bonds on the Screen.

3. Disulfide Bridges

Displays the Disulfide Bridges on the Screen.

4. Background

Changes the Background to white.

5. Lighting

Decreases the molecules light.

6. Show Axes

Displays the X,Y,Z axes on the Screen.

7. Show Bound Box

Displays a Bound Box on the Screen.

8. Labels

Displays the molecule's Labels.

10. Secondary Structure

Colors the three different states of Secondary Structure (a-helix, b-sheet, turns).

10. Wireframe Model

Alters the representation mode to Wireframe Model.

11. Spacefilling Model

Alters the representation mode to Spacefilling Model.

12. Dots Model

Alters the representation mode to Dots Model.

13. Ribbon Model

Alters the representation mode to Ribbon Model.

14. Strands Model

Alters the representation mode to Strands Model.

15. Cartoons Model

Alters the representation mode to Cartoons Model.

4.1.2 Calculations Panel

1. Distance

By clicking on 'Distance' the user can calculate the distance between two selected atoms.

2. Angle

By clicking on 'Angle' and by then selecting three atoms the user can calculate the Angle between them.

3. Torsion

By clicking on 'Torsion' and by then selecting four atoms the user can calculate the Torsion Angle.

4.1.3 Rotations Panel

1. Zoom

Increases or decreases the Molecule's Zoom.

2. Rotate X

Rotates Around X axis.

3. Rotate Y

Rotates Around Y axis.

4. Rotate Z

Rotates Around Z axis.

5. Move X

6. Move Y

7. Move Z

8. Around Atom

By clicking on the (+) button and by selecting one atom the program can perform rotations around the atom selected. The (-) button cancels the previous selection.

4.1.4 Aminoacid Groups Panel

1. Positive

Colors the Positive aminoacid group.

2. Negative

Colors the Negative aminoacid group.

3. Aromatic

Colors the Aromatic aminoacid group.

4. Aliphatic

Colors the Aliphatic aminoacid group.

5. Polar

Colors the Polar aminoacid group.

6. Hydrophobic

Colors the Hydrophobic aminoacid group.

7. Reset

Resets the model.

4.1.5 Report Bar

The Chemscape Chime plugin version 2.0.2 can give information about the atoms selected by the user. The selection can be done using the left mouse button. When the user clicks an atom in the Report Bar appears:

where:

str1 : Name of the Atom Selected

n1 : Number of the Atom Selected

str2 : Residue name

n2 : Residue number

By clicking on two atoms when the 'Distance' button is activated the distance between those atoms appears in the Report Bar:

where:

str1 : Residue name

n1 : Residue number

str2 : Name of the 1st Atom

n2 : Atom number

D : Calculated Distance

By clicking on three(or four) atoms when the 'Angle'(or the 'Torsion Angle') button is activated the Angle(or the Torsion Angle) between those atoms appears in the Report Bar:

where:

str1 : First Atom's Residue name

n1 : First Atom's Residue number

str2 : First Atom's name

n2 : First Atom's number

str3 : Second Atom's Residue name

n3 : Second Atom's Residue number

str4 : Second Atom's name

n4 : Second Atom's number

A : Calculated Angle

4.2 Text Mode

The text output gives the PDB file in text mode. The user can copy and paste the text to a text editor and save it as PDB file. The he can use any Molecular Graphics Program to view the structure created by S.C.A.R.

4.3 Appendix