When Artemis is started it will attempt to read a file called options from the current directory. If this file exists it should contain option settings that look like this:
option_name = option_valueIf the value of an options is too long to fit on one line it can be split over several lines by ending each line with a backslash like this:
option_name = option_value another_option_value \ a_third_option_value a_forth_option_value
Here are the possible options:
This option will set the font size for all the Artemis windows. The default font size is 14.
This option is used to set the minimum size of a "large" open reading frame, which controls which ORFS are marked by the "Mark Open Reading Frames" menu item (see the section called Mark Open Reading Frames in Chapter 3).
This contains a list of keys (separated by spaces) that are allowed in addition to those specified by EMBL. The official EMBL keys are listed in the feature_keys file in the Artemis code directory.
This contains a list of qualifiers (and their associated type) that are allowed in addition to those specified by EMBL. The official EMBL qualifiers and qualifier types are listed and described in the qualifier_types file in the Artemis code directory.
This is a list of the keys that should be shown in the feature edit window. (see the section called Edit Selected Features in Chapter 3).
The feature colours (see the section called Feature Colours) used by Artemis can be changed using the options file. By default there are 12 possible colour (numbered 0 to 12). The option names for the colours are colour_0, colour_1, etc. The value of each of these qualifiers should be the three numbers separated by spaces. The numbers correspond to red, green and blue respectively and each number is an intensity from 0 to 255. As an example, to change colour 2 to white put this line in the options file:
colour_2 = 255 255 255
The default options in the file etc/options in the artemis installation directory. Here is an example options file which shows the defaults:
# this line is a comment font_size = 14 minimum_orf_size = 100 extra_keys = \ BLASTN_HIT CDS_BEFORE CDS_AFTER CDS_before CDS_after \ CDS_motif BLASTCDS extra_qualifiers = \ fasta_file "text" \ blast_file "text" \ bicsw_file "text" \ label text \ colour text \ class "text" common_keys = \ allele attenuator CDS conflict exon intron LTR misc_feature misc_RNA mRNA \ mutation polyA_signal polyA_site promoter protein_bind RBS repeat_region \ repeat_unit rRNA scRNA snRNA source stem_loop STS TATA_signal terminator \ tRNA unsure variation -10_signal -35_signal