You can also select TLS (translation, libration and screw-rotation) with restrained refinement, however I would suggest running a couple rounds of normal restrained refinement before starting to play with TLS. If you are just beginning a refinement round you want to select 'rigid body refinement' for your first refinement round, however after this you will probably need to be running restrained refinement. This can be selected by clicking on the 'Do restrained refinement' tab which will give you the following drop-down menu:
Starting at the top of the menu you need to give your job a title (something you will be able to remember), and then select the type of refinement you would like to perform.
To open the program click on the yellow tab in the top left corner of the ccp4i GUI, select 'Refinement' and then 'Run Refmac5'. It is written by Garib Murshudov at the University of York, and its web page can be found here. Refmac is a refinement program that comes bundled with ccp4i and is probably the easiest to use if you have just scaled and phased your data using ccp4.
