# EMBOSS COLOUR MAPS # # The format of this file should be fairly self-explanatory. # # We want to make it possible for programs which display residues and # bases in colour to have a standard set of colours to plot in. # # We also want the user to have the ability to select different colour # maps for different puposes or according to individual taste. # # We want to make it easy for users to add to or amend the colour maps. # # We want to be able to set colours for both the PLPLOT (rather # restricted) set of colours and for HTML which has a much larger set of # available colours, even if we keep to the 'Safe PC/Mac WWW colours' # # Comment lines start with a '#'. # # Columns are separated by white space (one or more tabs and/or spaces) # # A colour map starts with the tag 'MAP' and is followed by the name of # that map. # # The default colour to use in that map is specified by 'default:' # followed by the colour for PLPLOT. # # The colours of the characters for the bases or residues are specified # as for the 'default:' tag. The characters are case independent. # # Any characters whose colour has not been specified will use the # default colour. # # The available PLPLOT plotting colours are: # "BLACK", "RED", "YELLOW", "GREEN", "AQUAMARINE", "PINK", "WHEAT", # "GREY", "BROWN", "BLUE", "BLUEVIOLET", "CYAN", "TURQUOISE", "MAGENTA", # "SALMON", "WHITE" # Define the colours as hexadecimal Red/Green/Blue values. # This doesn't affect plotting device colours, only HTML colours. # # These are the nearest Safe PC/Mac WWW colour to the Netscape colour # name. They are all acceptable except for 'wheat' (F5E4C5). I left it # as FFFFCC, which is more of a light-yellow than I would like, but it # will do as a default. # # Useful colour palattes: # http://www.iconbazaar.com/color_tables/named_colors.php # http://www.hidaho.com/colorcenter/cc.html COLOUR BLACK 000000 COLOUR RED FF0000 COLOUR YELLOW FFFF00 COLOUR GREEN 00FF00 COLOUR AQUAMARINE 99CCFF COLOUR PINK FFCCCC COLOUR WHEAT FFFFCC COLOUR GREY 999999 COLOUR BROWN 993300 COLOUR BLUE 0000FF COLOUR BLUEVIOLET 9933FF COLOUR CYAN 00FFFF COLOUR TURQUOISE 33FFCC COLOUR MAGENTA FF00FF COLOUR SALMON FF9966 COLOUR WHITE FFFFFF # The null map - everything is black MAP none [ default: BLACK ] # These are the colours used in trace displays in many base-calling # # packages. # I think this is the closest we come to standard base colours. MAP nucleic [ default: GREY A: GREEN C: BLUE G: BLACK T: RED ] # EMBOSS Standard protein colours. # # [These are two possibilities for their origin. Many years ago there # was a discussion on the bionet newsgroups about colours. There was also # a suggested colour scheme from Toby Gibson (then at EMBL, Heidelberg). # Toby is colour-blind so there may be some slightly unusual choices. # - Peter Rice] MAP protein [ default: BLACK DE: RED HKR: BLUE G: GREY A: BLACK CMU: YELLOW ST: CYAN NQ: GREEN LVI: BLACK FWY: WHEAT P: BLUEVIOLET ] # Rasmol colours # # The following colour scheme is an approximation to the RasMol amino # colour scheme, colouring them according to traditional amino acid # properties. The purpose of colouring is to identify amino acids in an # unusual or surprising environment. # # The outer parts of a protein that are polar are visible colours and # non-polar residues are darker. MAP rasmol [ default: BLACK DE: RED FY: BLUE KR: BLUEVIOLET G: GREY A: BROWN H: AQUAMARINE CMU: YELLOW ST: SALMON NQ: CYAN LVI: GREEN W: PINK P: WHEAT ] # GCG SeqLab colours # Some people like this for some reason... MAP gcg [ default: BLACK FYW: RED HN: BROWN IVLM: MAGENTA CASTU: YELLOW G: SALMON BDEZ: GREEN Q: TURQUOISE KR: BLUE P: CYAN ] # Acidic/Basic (Red=acidic, Blue=basic) MAP acidic [ default: BLACK DE: RED RKH: BLUE ] # Polar (Red=Polar) MAP polar [ default: BLACK RNDQEHKSTWY RED ] # Hydrophobic (Red=Hydrophobic) MAP hydrophobic [ default: BLACK ACGILMFPSTWYV: RED ] # Aromatic/Aliphatic (Red=Aromatic, Blue=Aliphatic) MAP aromatic [ default: BLACK HFWY: RED ILV: BLUE ] # Surface/Buried (Red=Surface, Blue=Buried) MAP buried [ default: BLACK RNDEQGHKPSTY: RED ACILMFWV: BLUE ] # Positive/Negative charge (Red=Positive, Blue=Negative) MAP charge [ default: BLACK RHK: RED DE: BLUE ] # Tiny/Small/Large (Red=Tiny, Green=Small, Blue=Large) MAP size [ default: BLACK AGS: RED NDCPTV: GREEN REQHILKMFWY: BLUE ] # Safe PC/Mac WWW colours # ----------------------- # # To be browser safe, for RGB you can use 0, 51, 102, 153, 204 or for # hexadecimal 255 or 00, 33, 66, 99, CC, and FF in any combination in the # three slots. So 153 0 102 is the same as 990066 and produces a reddish # purple. # # #Rasmol Amino Colours #-------------------- # #The RasMol `amino' colour scheme colours amino acids according to #traditional amino acid properties. The purpose of colouring is to identify #amino acids in an unusual or surprising environment. The outer parts of a #protein that are polar are visible (bright) colours and non-polar residues #darker. Most colours are hallowed by tradition. This colour scheme is #similar to the `shapely' scheme. # # ASP,GLU bright red [230,10,10] CYS,MET yellow [230,230,0] # LYS,ARG blue [20,90,255] SER,THR orange [250,150,0] # PHE,TYR mid blue [50,50,170] ASN,GLN cyan [0,220,220] # GLY light grey [235,235,235] LEU,VAL,ILE green [15,130,15] # ALA dark grey [200,200,200] TRP pink [180,90,180] # HIS pale blue [130,130,210] PRO flesh [220,150,130] # # #Rasmol Structure Colours #------------------------ # #The RasMol `structure' colour scheme colours the molecule by protein #secondary structure. Alpha helices are coloured magenta, [240,0,128], beta #sheets are coloured yellow, [255,255,0], turns are coloured pale blue, #[96,128,255] and all other residues are coloured white. The secondary #structure is either read from the PDB file (HELIX and SHEET records), if #available, or determined using Kabsch and Sander's DSSP algorithm. The #RasMol `structure' command may be used to force DSSP's structure assignment #to be used.