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.