A: Press 'Left button' on the mouse, keep it pressed and move the mouse around. This will rotate structure around the axis in the plane of a screen. Press 'Shift' and 'Right button' on the mouse, keep them pressed and move the mouse around. This will rotate structure around the axis perpendicular to the screen.

A: Press 'Shift' and 'Left button' on the mouse, keep them pressed and move the mouse forward and backward.

A: Press 'Right button' on the mouse, keep it pressed and move the mouse around. You will move structures along with the the internal center of the picture.

A: Press the "target" icon in the left toolbar or type command 'center' in 'Friend command line'. The picture will centered to the current internal center. By default it is placed in the center of the screen but movements of molecules move it too. See previous question.

A: Use menu 'Select' or command 'select' (type 'help select' in Friend command line to get more information about usage) to select a fragment of a protein. Use menu 'Display' to change the representation, and use menu 'Color' to change the color. Usage of menus is described in 'Help->Documentation'. One can also change the color and representation of residues by clicking on them in 'Sequence alignment window'. Select the mouse mode in the 'Sequence alignment window' by choosing mode in the right drop-down menu (by default it is set to 'Edit'). Then click on the residue in 'Sequence alignment window'. For example, to change color of residues select 'Highlight' and click on the residues you want to change color.

A: Mark two sequences by clicking on their names in 'Sequence alignment window'. The names must br highlighted. Use menu command 'Tools->Pairwise->Align' to align sequences. This will bring a new window with sequence alignment. Use button 'Load to alignment editor' to load alignment into 'Sequence alignment window'.

A: Mark two sequences by clicking on their names in 'Sequence alignment window'. The names must highlighted.  Use menu command 'Tools->TOPOFIT->Align' to align structures corresponding to the marked sequences.

A: Mark two sequences by clicking on their names in 'Sequence alignment window'. The names must highlighted.  Use menu commands 'Tools->Fit by alignment->...' to superimpose structures based on the current sequence alignment.

A: Use submenu 'Export' in menu 'File'.

A: Use menu command 'File->Copy' to copy image to the clipboard (copying to the clipboard is available only on Windows platform). In your Microsoft Word document paste the image from the clipboard.

A: Mark sequences related to the structures you want to be seen. Marking is made by clicking on the sequence names in 'Sequence alignment window'. The names must highlighted. Use menu command 'Visible->Marked chains only' to view only structures for marked chains.

A: Use menu command 'File->Load->Alignment from file' to load alignment files. Currently supported alignment formats are PIR, FASTA, SKY, CEA, CLUSTAL. More information about loading alignemnt files can by found in menu 'Help->Documentation' and here.