6.7 Add fragments
VEGA ZZ has the capability to add entire new fragments.
It's based on the
powerful integrated database engine that allows the use of standard fragment
libraries and the creation of personalized too. These features increment the
user productivity due to fast molecule building.
Selecting the Edit -> Add -> Fragments menu item, the following
wizard is shown:
As first step, you must select the Group library and the Fragment. The library is automatically opened clicking on the group name. If the Inherit residue name option is checked, the added fragment inherits the residue name, the residue number and the chain ID from the main molecule. Checking Inc. residue number, the residue number is automatically incremented starting from the specified number every time as a new fragment is added. That's useful building a biopolymer.
When you click on the fragment name, its 3D structure is shown in the main window. Select where to place the fragment in the atom list (After the selected atom, at residue end and at the molecule end). Press the Next button to continue.
Now you must click a fragment hydrogen in the main window that will be merged with another molecule hydrogen in order to build the bond. Press Next to continue.
Selecting the molecule hydrogen and the Next button the bond will be completed.
At the end, you can adjust the torsion
angle between the molecule and the fragment clicking the torsion buttons. Click
the Finish to place definitively the fragment. Now the tool is ready to
bind another fragment to the molecule.
Please remember that when the workspace is empty (no molecule loaded), the first
wizard step is operative only and the Previous button, when active,
allows to go to the previous wizard step.
The fragment libraries are zip files placed in the Data/Fragments folder and they are created by the Database Explorer. You can use this tool to change/expand the standard database. The preferred molecule file format to use in these libraries is the IFF, because it can contain the best number of information.