Table of contents
What is the Editor ?
Nonribosomal Peptide Editor is a Java applet that allows the user to
easily draw a monomeric stucture, i.e. amino acids and links
between them representing the nonribosomal peptide.
It can be used to draw parts or an entire peptide structure to search
for in the database.
The structure can be completely created, or the user can choose to
modify an existing one.
Once the structure is obtained, it is transformed into a text version so
that the user can launch a structural search with it.
In this editor, the monomers or clusters are represented as boxes and the chemical bonds between them by links.
- Add a monomer or a cluster of monomers: to add a box representing a monomer or a cluster to the drawing area you can either select in the available catalog, on the left part of the editor, one monomer, one cluster name or several monomers (clusters) by pushing the "Ctrl" or "Maj" buttons when cliking. Then click on the "add" button. Then click on the drawing area to put it wherever you want. In the catalog, behind each monomer name the number of peptides containing this monomer is given. When you select a monomer, its complete name appears in the text field at the top of the list.
- Press the "clear" button to clear your selection. Search for a monomer: The text field at the top of the catalog can be used to search for a monomer or a upper level of the hierarchy. While you start typing the monomer's name you are searching for, the tree will open at the appropriate position and the monomers matching the characters appear in red. The more characters you type, the more precise the search will be.
- Add a link: click on the "add link" button. Once the button is pressed, the cursor of the mouse is changed. To add a link, click the mouse on the starting box and release it on the ending one.
- Delete a box: click on the "delete monomer" button. Then click on the box you want to delete. When a monomer is deleted, all the links pointing this monomer are deleted too.
- Delete a link: click on the "delete link" button. Then click on the link you want to delete. The monomers associated with the deleted link will not be removed, they will just change color as they have lost a link.
- Move a box: press the mouse button on a box and move the cursor to a new location, then release the mouse button. Caution: be careful that another button is not pressed.
- Finish: once the peptide structure is completed, click on the "go" button. This returns the peptide structure to the Norine Database search page and you can launch a search with it.
- Reset all: Use the "edit" menu and choose "reset all". All the boxes and links are erased.
- Open a structure: use the "edit" menu and choose "open". You can open a file in Norine format (.nor). This type of file can be obtain from the visualization applet of Norine by selecting the 'save as text' option (click here to know more on the visualization applet) or from the editor . This will draw the opened structure and you will be able to modify it.
- Save the structure: you can save the structure you have drawn for further modifications or to use it an other time by choosing "save as text" in the "edit" menu. This will create a file in the Norine format (.nor).