This is the first window that opens when you start Artemis. The menus at the top of this window allow you to read a new sequence or embl entry.
If you select this menu item a file requester will be displayed which allows you to open a flat file containing an entry. If the file you select is successfully read a new window will open, which shows the sequence and features for the entry. See Chapter 3 to find out how to use the main window.
The functions will ask the user for an accession number and then will attempt to read it directly from the EBI using CORBA. If all goes well you will be presented with an view/edit window (see Chapter 3).
Please note that this feature is still experimental and is not be available on all platforms. The menu is currently disabled on Macintosh and Windows machines.
This menu item will close all windows and then exit the program
Choosing this menu item will discard the current options settings and then re-read the options file. Note that changing the font size in the file and then selecting this menu item will only change the font size for new windows, not existing windows. Currently some options are unaffected by this menu item. See the section called Options File Format in Chapter 4 for more information about options.
This menu item will toggle "direct editing" option. It is off be default because it can have surprising results unless the user is expecting it. See the section called "Direct Editing" in Chapter 3 for more detail about this.
If this toggle is on, Artemis will use the eukaroytic start codon (ATG). If this toggle is off it will use the prokaryotic start codons (ATG, GTG and TTG). This setting effects the display of start codons (see the section called Start Codons in Chapter 3) and the "Suspicious Start Codons ..." feature filter (see the section called Suspicious Start Codons ... in Chapter 3).
This can be set in the options file (see the section called organism_type in Chapter 4).
When this option is on and the "One Line Per Entry" is on (see the section called One Line Per Entry in Chapter 3) the line that the active entry is on will be highlighted in yellow.
Show the log of informational messages from Artemis. Currently the log window is only used on UNIX and GNU/Linux systems to show the output of external programs. This menu item is only available when running Artemis on UNIX or GNU/Linux systems.
Hide the log of informational messages. This menu item is only available when running Artemis on UNIX or GNU/Linux systems.