Editing enzyme files
TO ADD a new entry to an enzyme file
Entries can be added to an enzyme file at any time that the window for the file is active.
1. Open the required enzyme file, and ensure that the file window is active.
2. If the file is locked, unlock it by toggling the lock button.
3. Select the button labeled with a plus (+) sign.
The Enzyme Editor dialog box is displayed.
4. Type a name for the enzyme in the Name text box.
5. Click the sequence representation in the center of the dialog box to position the insertion point, then type the recognition site using the IUPAC one-letter codes.
For proteins, enter the recognition sequence in the amino to carboxy direction; for nucleic acids, in the 5' to 3' direction.
NOTE: Use parentheses to enclose a combination of amino acids for which there is no one-letter assignment. For example, if the agent cleaves after an aspartic (D) or glutamic (E) acid residue, denote it as (DE).
6. Drag the arrow-shaped control to the cut position.
For restriction enzymes, there are two arrows: the upper one to indicate the cut position on the plus strand, the lower one to indicate the cut position on the minus strand.
7. If required, you can enter a comment up to 254 characters long.
8. Select OK to add the enzyme to the file.
9. Choose File | Save to make the changes permanent.
TO COPY entries between files
Copying existing entries between files can be useful, for example to create a customized enzyme subset from more than one file. This requires that one or more enzyme files are open at the same time, and that the file receiving the enzyme entries is unlocked.
1. Make the file from which you are copying entries the active window.
2. Select the enzymes that you want to copy using one of the following methods:
- click to select a single entry
- hold down the mouse button and drag to select a continuous block of entries
- hold the shift key in combination with either of the above to retain already selected entries.
3. Choose Edit | Copy.
4. Make the file that is receiving the entries the active window.
5. If the file is locked, unlock it by toggling the lock button.
6. Choose Edit | Paste.
The entries are added to the file in alphabetical order.
7. Choose File | Save to make the changes permanent.
If any of the entries were marked as selected (with a check mark), the selection will be retained.
TO EDIT an enzyme entry
Entries in an enzyme file can be modified. This is generally useful only when a mistake has been noticed in the existing entry.
1. Open the required enzyme file, and ensure that the file window is active.
2. If the file is locked, unlock it by toggling the lock button.
3. Select the enzyme that you want to edit.
4. Select the button labeled with a delta sign.
The Enzyme Editor dialog box is displayed.
5. Modify the entry as required.
See To add a new entry to an enzyme file,above, for further details.
6. Select OK to add the changes to the enzyme file.
7. Choose File | Save to make the changes permanent.
TO DELETE an enzyme entry
Entries in an enzyme file can be deleted when required.
1. Open the required enzyme file, and ensure that the file window is active.
2. If the file is locked, unlock it by toggling the lock button.
3. Select the enzymes that you want to delete using one of the following methods:
- click to select a single entry
- hold down the mouse button and drag to select a continuous block of entries
- hold the shift key in combination with either of the above to retain already selected entries
4. Select the button labeled with a minus (-) sign.
The selected entries are deleted from the file.
5. Select File | Save to make the changes permanent.
NOTE: This is equivalent to using Edit | Clear. If you want to paste the deleted entries into another file, use Edit | Cut instead of the minus button.
Related Topics.
Automatic Restriction Enzyme Analysis