DYNAMO NMR Molecular Structure Engine
Creating Sequence Descriptions with the GMC Edit Interface
Introduction
The first step in a DYNAMO structure calculation is creation of the
definitions of covalent geometry for the molecular system. In DYNAMO,
these are stored as a series of NMRPipe-format tables with specific
names in a General Molecular Coordinate (GMC) directory. DYNAMO 2.1
includes an updated graphical interface program to create these molecular
definitions automatically from an interactively specified residue sequence.
To create a new GMC directory, type the command:
gmcEdit
Or, you can specify the name of an exiting or desired GMC directory
to edit, for example:
gmcEdit ubiq.gmc
DYNAMO molecular descriptions consist one or more segments. A segment
is a single protein or nucleic acid chain, or a group of separate
small molecules to be considered as a unit (for example, a collection
of water molecules).
The basic flow for creation of a molecule with one or more segments is
as follows:
-
NEW: Use the "New" button to create a new segment.
The newly created segment will have no residues.
-
SELECT: Use the mouse to selecy the new segment in the
"Segments:" window. The selected segment will be highlighted.
-
EDIT: Use the "Edit" button to edit the contents of the selected
segment. During editing, you will define the segment type,
(protein, dna, rna, other), the unique name for the segment,
the residue sequence, etc. More details about editing
a segment are given below.
-
SAVE: Use the "Save" button to save the values for this segment.
-
REPEAT: Stages 1-4 can be repeated to define additional segments
(note that each segment must have a unique name). Also,
existing segments can be adjusted again by using steps 2-4.
-
ADJUST: After the segments have been defined, special
adjustments to the molecular description such as
disulfide bonds can be defined.
-
GENERATE: Once all the segments and sequences have been defined,
use the "Generate GMC" button to create the GMC directory
and its contents.
-
QUIT: Use the "Quit" button to exit the graphical interface.
Editing a Segment
In the current version, the left side of the "gmcEdit" graphical
window is used to specify segments, and the right side of the
window contains a series of "tabs" listing the available residues types
which can be added to a given segment. There are also tabs for
modifications of a sequence, such as the addition of a protein
disulfide bond.
When editing a given segment, the typical steps are:
-
NAME: Give each segment a unique name in the "Segment Name:" field.
-
START: Assign a starting residue ID number for the segment
in the "Start ResID:" field.
-
TYPE: Set the segment's type (protein, DNA, RNA, or other) with
the given buttons.
-
SEQUENCE: Select the appropriate "tab" on the right to reveal
the available residue types ("Protein", "Nucleic Acid",
or "Other"). You can then add residues to the sequence
by clicking the residue name buttons in the order that
the residues occur in the desired sequence. Also:
-
The "Protein" tab has additional check boxes to
end the segment with an amine group on the N terminus
or an acid group on the C terminus (these boxes should
ordinarily be checked).
-
Nucleic acids have additional check boxes to add
phosphates to their 5' or 3' ends.
-
SAVE: Use the "Save" button as noted above to save the
changes made to the segment.
Generating the GMC Directory Contents
Once all the segment definitions are created and saved, use the
"Generate GMC" button to create the GMC diretory and contents.
Status messages will appear on the screen indicating the
progress of the procedure, which can take a minute or more.
When GMC creation is complete, the top border of the GMC Edit window
will display a "Done" message.
