Main Menu Reference
The File Menu
The File menu contains entries concerning loading/saving data
files in various formats and exiting the program.
- Load Prediction File
-
Shows a file selection dialog that allows loading a prediction file
in FASTA format, see Section 1.1.3.
If the selected file is a valid prediction file, the current protein
will be replaced with the protein created by reading the selected
prediction file.
-
Load Angle File
-
Shows a file selection dialog that allows loading a dihedral angle
file. If the selected file is a valid dihedral angle file and
matches the current protein, the dihedral angles stored in the file
are applied to the current protein.
-
Save Angle File
-
Shows a file selection dialog that allows saving a dihedral angle
file. If a filename is selected, the dihedral angles of all
currently active coil regions will be written to the selected file.
-
Load PDB File
-
Shows a file selection dialog that allows loading a PDB file, see
Section 1.1.3. If
the selected file is a valid PDB file, the current protein will be
replaced with the protein created by reading the selected PDB file.
-
Save PDB File
-
Shows a file selection dialog that allows saving a PDB file. If a
filename is selected, the current protein will be written to the
selected file. ProteinShop always includes secondary structure
comments when writing PDB files, see Section 1.1.3.
This means that the current protein can be exactly recreated by
reading the PDB file just written (up to the precision of cartesian
coordinates stored in PDB files, of course).
-
Quit
-
Exits the program. If the current protein has been manipulated, but
not been saved to a PDB file, ProteinShop will ask for confirmation
before exiting.
The Server Menu
The Server menu contains entries concerning the use of ProteinShop
as a front-end for a remote protein structure prediction process.
This menu, and the front-end functionality, is not useful if there is
no remote prediction server that understands ProteinShop's
communications protocol.
- Connect
-
Shows a dialog that allows connecting to a remote protein structure
prediction server using a compatible communications interface. When
connecting to a server, the current protein must match the protein
being worked on by the server. This can be ensured by first loading
a correct prediction or PDB file.
-
Disconnect
-
Disconnects from a currently connected prediction server. This does
not affect the current protein.
-
Get Optimization Tree
-
Downloads a graph of candidate protein structures from the server.
The graph will always be written out to a text file named
"OptimizationTree.txt".
-
Get Configuration
-
Shows a dialog that allows downloading a queued candidate
configuration from the remote server. The desired configuration's
index in the server queue can be specified with the "Configuration
index" slider.
-
Get Configuration by ID
-
Shows a dialog that allows downloading a candidate configuration
from the server using its unique ID number. The desired ID can
be entered into the "Configuration ID" text field.
-
Get Best Configuration
-
Downloads the "best" configuration currently in the
server's queue.
-
Add Current Configuration
-
Re-submits the current protein to the remote prediction server for
future consideration.
The Edit Menu
The Edit menu contains entries to access ProteinShop's Undo/Redo
functionality, see Section x.y.z.
- Undo
-
Undoes the last atomic manipulation on the current protein.
-
Redo
-
Redoes the last undone atomic manipulation on the current protein.
The View Menu
The View menu contains entries concerning viewpoint navigation,
see Section 1.2.2.
- Center View
-
Resets viewing parameters, see Section 1.2.2.
-
Save Current View
-
Saves the current viewing direction, position, and orientation.
-
Restore Saved View
-
Restores the saved viewing direction, position, and orientation.
-
The Tool Menu
- The Tool menu contains entries that permit to
toggle the visibility of the BuildBeta and Copy dialog.
BuildBeta
-
Toggle visibility of the
BuildBeta Dialog.
Copy
Toggle
visibility of the Copy Dialog. Selected residues will be duplicated
to create a new fragment with the same name as the protein structure being copied. A single secondary
structure will be duplicated if a secondary second structure is
selected.
The Windows Menu
The Windows menu contains entries that permit to toggle the
visibility of several program dialogs.
- Show Residue Dialog
-
Toggles visibility of the Residue
Dialog.
-
Show Structure Dialog
-
Toggles visibility of the Structure
Dialog.
-
Show Sequence Dialog
-
Toggles visibility of the Sequence Dialog.
-
Show Ramachandran Plot Window
-
Toggles visibility of the Ramachandran
Plot Window.
-
Show Drawing Toggles Dialog
-
Toggles visibility of the Drawing
Toggles Dialog.
-
Show Selection Dialog
-
Toggles visibility of the Selection
Dialog.
-
Show Energy Visualization Dialog
-
Toggles visibility of the Energy
Visualization Dialog.
The Help Menu
- About ProteinShop
-
Shows a message box with copyright and contact information.