So here we go….
Scroll Bars The scroll bar across the bottom of the canvas area is used to rotate the molecule about the y-axis, i. Each scroll bar has an 'indicator' to denote the relative orientation of the molecule, which is initially positioned in the centre of the scroll bar.
These scroll bars may be operated in either of two ways.
The first is by clicking any mouse button on the dotted scroll bar background to indicate a direct rotation relative to the current indicator position; the second is by clicking one of the arrows at either end of the scroll bar to rotate the molecule in fixed sized increments.
Rotating the molecule by the second method may cause the indicators on the scroll bars to wrap around from one end of the bar to the other. A complete revolution is indicated by the indicator travelling the length of the scroll bar.
The angle rotated by using the arrows depends upon the current size of the display window. The normal behavior of the scroll bars can be changed by the ' rotate bond ' and ' rotate all ' commands and restored to normal operation by the ' rotate molecule ' command. Alternatively the equivalent items in the "Settings" menu may be used.
When ' rotate bond ' is selected, the bottom scroll bar controls. When ' rotate all ' is selected, the scroll bars control rotation of all the loaded molecules instead of just rotating the currently selected molecule.
Picking In order to identify a particular atom or bond being displayed, RasMol allows the users to 'pick' objects on the screen. The mouse is used to position the cross-hair cursor over the appropriate item, and then any of the mouse buttons is depressed.
Provided that the pointer is located close enough to a visible object, the program determines the identity of the nearest atom to the point identified. The program will display, in the terminal window, the atom's type, serial number, residue name and residue number.
If the atom is a member of a named chain, the chain identifier is also displayed. Two examples of the output generated by selecting an atom are displayed below: P The first line describes the alpha carbon of the serine amino acid in a protein.
The unique Protein Data Bank serial number for this atom is The following line describes the oxygen atom in a water molecule attached to the P chain of the main molecule. The word 'Hetero' distinguishes heterogeneous molecules such as cofactors from the residues in the main molecule, noted by 'Group'.
O', respectively, when using the RasMol commands 'select' and 'restrict'. See the ' set picking ' command for details. Dials Box If RasMol detects a 'dials box' attached to the user's workstation, it also allows the molecule to be manipulated interactively by the dials.
Rotating any of the knobs will automatically transform and redisplay the molecule interactively.
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The dials only have effect while the mouse pointer is within the display window. If more than one application is using the dials box at a time, care must be taken to remember the dial labels assigned by each program, as each application may overwrite the dial-label LEDS.
The rotation about the X and Y axes automatically updates the indicators on the appropriate scroll bars. All the rotation dials rotate the molecule degrees for a complete revolution of the dial. All the remaining dials clamp their values to permissible ranges; turning these dials past their limits has no effect.
The centre of rotation of the molecule may be changed using the ' centre ' command on the command line, or the command ' set picking centre ' followed by a mouse click.Chemistry: An Introduction to General, Organic, and Biological Chemistry, Books a la Carte Plus Mastering Chemistry with Pearson eText -- Access Card Package (13th Edition) 13th Edition.
Author Item Language Isabel Serván Martínez, José Miguel Fernández Fernández Manual: Spanish José Miguel Fernández Fernández: Manual. 2 TP 8/05 CAUTION Caution: To reduce the chance of personal injury and/or property damage, carefully observe the instructions that follow.
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