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.
Selecting this shows the files and directories that are in the directory Artemis is launched from. The user home directory and the current working directories are shown and can be navigated.
This opens a window displaying a local file manager at the top and login options to access a remote file system via Secure Shell (SSH). When the login details are typed in and 'Connect' pressed the bottom half of the window will display the other (remote) file system. See Chapter 4 to find out how to use this and how to set up the connection.
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 Dbfetch. If all goes well you will be presented with an view/edit window (see Chapter 3).
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 5 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.
These options make all the NCBI Genetic Codes available. The default setting is the Standard Code. 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 is an advanced option for sites that have set up the ability to submit searches via SSH to another machine.
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.