The peptide display allows the user to display peptide sequences attached to protein objects. In order to invoke it's use within ACEDB the following lines/declarations must be in the following files :

displays.wrm

_DPEPMAP -g TEXT_FIT -t Protein -y (x) -w (y) -height (z)

where x,y,and z are user defined sizes, usually between 0.1 and 1.0.

If the above line is missing the error message says :

internal system error : Geometry of PEPMAP is missing. Please edit wspec/display.wrm. Quit and restart acedb.
 
 

Data Format

To enter peptide data into the database the .ace file entries should look as follows :
 
Peptide PIR:A31142
VXDHPEFEKAGKDPGLQXWRFISKMGYPKQ
TQVQVLPESGETPLFKQFFKNWRDKEATDG
MGVAYVPNHIAKIENVPFDVTVLHESPAMA
AQHGMVDDGSGKKQIWRIENCEKVPVLESH
YGQFYGGDSYIILYHYKSGGKQGQIIYTWQ
GDDSTKDEITASAILSAQLDEELGGGPVQV
RVVQGKEPAHLISLFGGKPMIIYKGGTSRE
GGQTKDANVRLFQVRTSSSGFSRAVEVDNT
ASNLNSNDAFVLTTPSASYLWVGQGSTNVE
KNGAKELLKILGVSASEIPEGQETDDFWGA
LGGKADYRTSARLKDKLNAHPPRLFACSNK
TGRFIIEEVPGEISQDDLATDDVMLLDTWD
QVYVWVGNEAQEDEKKEAIASAYKYIESDP
ANRDKRTPVAITKQGFEPPTFIGWFLGWEA
DYWDVDPLERAMAGLSS

This reads the peptide sequence into an array class which is accessed directly by the display code. The Peptide class does not have to be defined in the model.

Peptide Display Features
 

The image shows a basic peptide display showing the columns presented without any analytical data attached.  The columns are user configurable by the same coloumn control system in use for the genetic map displays.

Header Buttons
 

Active Zone - This allows the user to select where the active zone for the peptide sequence analysis tools operate. It can be set by either typing the values into the yellow field to theright of the button or clicking and dragging within the Peptide sequnce column. right clicking on the Active Zone button allows a FASTA dump of the sequence defined as the Active Zone.

Views... - This tyakes the user to the View configuration display screen where the order of columns and what is shown on the display can be determined.

Whole, Zoom in and Zoom out - These buttons control the amount of the sequence that is being viewed. Whole shows the whole sequence, Zoom in increases the magnification by a factor of 2 and Zoom out decreases the magnification by a factor of 2.

Analysis... - This is a drop down menu controlled by the right mouse button. The analysis tools available are limited to self dotplot in the Dotter and FASTA dumping the active zone. Hopefully more functions/analysis tools will be added to this menu soon.

Column Display Area

From left to right we have the locator bar, scale, active zone indicator, peptide sequence and hydrophobicity columns. Analytical data such as BLAST homologies appear to the right of the hydrophobicity column. Each column has it's own set of user definable options which are shown by left clicking on the colummn name in the horizontal green bar at the bottom of the screen.
 
 Display Configuration Options
Standard view options to configure column order etc.

Column configuration options are listed below :
 

COLUMN	OPTIONS	EFFECT
Locator	Magnification	Not properly configured for the peptide display. Not really useful.
	Show Projection Lines	Draws guide lines from the ends of the locator bar to hte ends of the scale bar.
Scale	Scale Unit  Cursor Unit  Show Cursor	Three options that seem to do very little with the scale bar.(I couldn't work out what they do to it's appearance.
Peptide Sequence	Colour Residues & Default Colours	These options allow the user to highlight particular residues in a colour of thier choice (some 32 in all). There are two sets of predefined colours and each residue can be coloured by the use as desired.
	Residues per Wrap	This allows the user to configure the number of residues that are shown across the width of the Peptide Sequence column. Numbers between 0 and 1 are not valid and negative numbers send the machine thinking about what to do.
Hydrophobicity	Show Zero Bar	Draws the bar correponding to 0 on the display.
	Fixed Scaling	Fixes the two scaling numbers to -2.0 on the left and 2.0 on the right.
	Hydrophobicity Calculation Window	Alters the scale on which the hydrophobicity is calculated.
	Hydrophobicity Display Width	Changes the width of the display column.
Blast Homology Details	Homolname Display Width	Configures the amount of space given for the display of BLAST homology information for the displayed sequence
	Bump	Normal bump type behaviour, ie separates the information in the column to a fixed width.

 
Information on how to display multiple peptide sequences will appear once I've figured it out. This will have to wait till after I get back to Norwich.

Comments to :

Ben Arnold.