Type cosmic and press return. This will start Cosmic running.
Always watch the message window. Information and questions appear here. If Cosmic needs some information, you can type it here, but only if the mouse pointer is in this window. Cosmic has five modes: DRAW, VIEW, SURGERY, GEOMETRY and FIELD.
This mode is used to input molecules for the first time. Draw a molecule by clicking with the left hand mouse button. The left hand column of buttons allow you to select different atom types. If you want to alter a structure that has already been drawn, you must use the SURGERY mode.
Cosmic will calculate the positions that it expects hydrogen atoms to be, when you click on Add H.
Rotation
To rotate the molecule, click on Rotate, which is at the lower right- hand corner of the graphics window. This will hide all the buttons. Holding down the right hand mouse button and moving the mouse will rotate the molecule. Moving the mouse from left to right rotates the molecule around the y-axis; moving it up and down rotates around the x-axis. Hold down the middle button to rotate around the z- axis. Holding down the left hand mouse button will rotate the molecule towards the mouse pointer. Clicking anywhere outside the central box will return you to the draw mode.
Energy Minimisation
The energy of the molecule can be minimised by clicking on Charge/Minimise. You will be asked various questions which must be answered by typing on the keyboard, whilst the mouse is in the message window. Every question can be answered by simply pressing Enter to get the default response.
By default, Cosmic does not allow for any electrostatic effects. If you have polar groups in the molecule, you must tell it to add charges. This is one of the questions that you are asked when you select Charge/Minimise.
This mode has various options for reading molecules from files, and displaying their properties. In the VIEW mode, you can rotate the molecule simply by clicking in the graphics window. The mouse buttons behave in the same way as in the DRAW mode.
This mode allows you to edit a structure that has already been created in the DRAW mode, or read in from a file.
Enter this mode to measure atomic separation, bond angles and so on. An option is also available to calculate the absolute configuration of chiral centres.
This mode is for the calculation and manipulation of molecular electrostatic fields (See Practical Three, part (3)).
