Dialog Window Reference

The Residue Dialog

The Residue Dialog, see Figure 1, displays information about the currently selected amino acid residue, and allows changing some residue parameters.


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Figure 1: The Residue Dialog. (a) No residue is selected. (b) Some residue inside either an alpha-helix or a beta-strand is selected. (c) Some residue inside a coil region is selected. (d) Labels are enabled for the selected residue. (e) Residue colorings are enabled.

Residue index slider
This slider shows the index of the currently selected residue (or -1 if no residue is selected), and can be used to select a residue by dragging the slider with the mouse. Residue index is actually a misnomer, since the displayed number is not the residue's index in the residue chain, but the identification number that would be written out in a PDB file. Since residue numbers in PDB files are usually sequential and zero- or one-based, this is not too much of a distinction.
Residue type
This (unselectable) drop box displays the type of the currently selected residue, or "Unknown" if the residue is not one of the standard amino acids.
PDB file name
This text field shows the three-letter abbreviation that would be written to a PDB file to identify the current residue's type.
Structure type
This drop box shows the secondary structure type (alpha-helix, beta-strand, coil region) currently associated with the selected residue. Structure types can be assigned individually to each residue by selecting the desired type from the drop box. Reassigning a residue's type will implicitly change the current protein's secondary structure chain, and will select the new secondary structure containing the selected residue as the current residue. Changing a residue's structure type will not automatically set the residue's dihedral angles to the standard values for the new residue type. This can be achieved by selecting the "Reset to Standard" button in the Structure Dialog.
Dihedral Angles
These two text fields show the current dihedral angle values for the selected residue in degrees.
Randomize Angles
If the currently selected residue's structure type is coil region, this button will set the selected residue's dihedral angles to random values, uniformly distributed over the half-open interval [0, 2*pi).
Residue Label Toggle
The residue name, chain or model id, and residue id of the selected residue can be displayed or hidden on the screen.
Atom Label Toggle
All the name of atoms in the selected residue can be displayed or hidden on the screen.
Dihedral Angles Label Toggle
The current dihedral angle values for the selected residue in degrees can be displayed or hidden on the screen.
Residue Color Button
Three types of residue color ( hydrophobic, hydrophilic and disulfide) can be assigned to the current protein's residues based on the residue type. The default color for hydrophobic type is white. The default color for hydrophilic type is blue. The default color for disulfide type is yellow. All three types of residue color can be changed to different colors by editing the ProteinRenderer section in ProteinShop.cfg file.


The Structure Dialog

The Structure Dialog, see Figure 2, displays information about the currently selected secondary structure, and allows changing the global shape of the selected beta-strand and resetting all dihedral angles inside the selected structure to their standard values.




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Figure 2: The Structure Dialog. (a) No secondary structure is selected. (b) Either an alpha-helix or a coil region is selected. (c) A beta-strand is selected.

Structure index
This slider shows the index of the currently selected secondary structure (or -1 if no structure is selected), and can be used to select a secondary structure by dragging the slider with the mouse.
Structure type
This (unselectable) drop box displays the selected structure's type (alpha-helix, beta-strand, coil region).
Residue Index Range
These two text fields show the residue indices of the first and last residue contained in the selected secondary structure. The residue indices displayed here are the same ones as displayed by the "Residue index" slider in the Residue Dialog.
Beta Strand Shape Adjustment
If the selected structure is a beta-strand, these four rollers can be used to globally modify the selected beta-strand's shape. The four rollers correspond to the four basis vectors of the 2D shape parameter space. Counting residues inside a beta-strand beginning with zero, residue dihedral angles phi and psi are affected as follows:
B-strand curl
Dragging this roller to the right decreases phi and increases psi for even-numbered residues and increases phi and decreases psi for odd-numbered residues.
B-strand twist
Dragging this roller to the right increases both phi and psi for even- and odd-numbered residues.
B-strand pleat
Dragging this roller to the right decreases phi and increases psi for even- and odd-numbered residues.
B-strand braid
Dragging this roller to the right increases both phi and psi for even-numbered residues and decreases both phi and psi for odd-numbered residues.
Flatten B-strand
If the selected structure is a beta-strand, this button will set its dihedral angles to values such that all its hydrogen bond sites are coplanar. Aligning two flattened beta-strands allows forming arbitrary numbers of hydrogen bonds between them.
Reset to Standard
This button will reset the dihedral angles of all residues inside the selected structure to the standard values for the selected structure's type. Reassigning a residue's structure type using the Residue Dialog will not automatically set that residue's dihedral angles to the new standard values; this can be done on a per-structure basis with this button.

The Drawing Toggles Dialog

The Drawing Toggles Dialog, see Figure 3, is used to select rendering modes as desribed in Rendering Features. The dialog shows the global rendering mode settings, and per-structure settings for the currently selected secondary structure.




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Figure 3: The Drawing Toggles Dialog. (a) No secondary structure is selected. (b) Some secondary structure is selected.

Global Parameters
The toggle buttons in this group are used to toggle global rendering mode settings.
Structure Parameters
The toggle buttons in this group are used to toggle rendering mode settings for the currently selected secondary structure.

The Protein Selection Dialog

The Protein Selection Dialog, see Figure 4, is used to make selection and comparison between different proteins.




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Figure 4: The Protein Selection Dialog. (a) One protein is selected. (b) Two proteins are selected and the Align button is enabled.

Protein
All loaded protein names are displayed. The current (selected) protein name is highlighted.
Remove Button
The selected protein will be removed.
Center View Button
The selected protein will be moved to center of screen.
Align Button
Two proteins can be aligned for comparison and the RMSD value can be computed. The Align button is enabled when the second protein is selected by holding down the <Ctrl> modifier key and clicking the second protein's name. The color of the second protein will be grayed out. Three type of alignment can be performed: all atoms (check button A), backbone atoms only (check button B) and C-Alpha atoms only (check button C).
Position
Dragging each roller to move the selected protein along the X, Y or Z axis.
Orientation
Dragging each roller to rotate the selected protein along the X-Y, Y-Z or X-Z axis.

The Energy Visualization Dialog

The Energy Visualization Dialog, see Figure 5, is only available if an energy computation plug-in has been loaded. It displays the total internal energy of the current protein, and allows selecting energy components and value mapping ranges for energy visualization. From the Energy Visualization Dialog, you can open the Volume Rendering Dialog, which provides controls for the volumetric rendering of protein energy. The Energy Visualization Dialog looks like this:



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Figure 5: The Energy Visualization Dialog. The currently loaded energy computation library is AMBER with no solvation term.

Internal energy
This text output field displays the total energy value that was returned by the last energy calculation on the current protein.
Recalculate
This button causes immediate recalculation of the current protein's internal energy.
Run Local Optimization
If the energy plug-in provides local optimization, this button will invoke it. Press again to stop the minimization process.
Show Volume Rendering Dialog
Press this button to show the Volume Rendering Dialog, which provides controls for rendering atom energies superimposed on the molecular geometry.
Load Minimization Record
This button is disabled when a minimization record is loaded. When enabled, clicking it will open a file dialog in which a minimization record file can be specified. If a compatible file is loaded, the Record Dialog will display.
Visualize energy
This control toggles rendering of atom energy, using color-coding of atom spheres and volume texture, if the latter has been generated.  For the color-coding of atom spheres, the van-der-Waals sphere of each atom inside the current protein will be colored according to that atom's partial internal energy value. To have visible effect, the current rendering mode has to include van-der-Waals sphere rendering, Section 1.2.1.
Display energy
This control toggles display of the energy value on screen.
Sec
This filed is used to change the interval of time for the update of the energy value during a manipulation.
Record minimization states to file
If the energy plug-in provides local optimization, this toggle will save the atom positions, energy states, and force field gradients to a binary file with each iteration of the minimization process. The name of the record file is defined in the configuration file. Any record previously stored in the record file will be overwritten by the new record, so it is a good idea to rename record files that you want to keep. Be advised that record files can quickly become very large; about (48 + 8C) * N bytes per iteration, where C is the number of energy component terms supported by the energy plug-in, and N is the number of atoms in the molecule. The number of iterations can easily reach into the tens of thousands. They often do not compress well, either. Once generated, records can be accessed through the Record Dialog.
Energy Mapping Range
These fields are used to define the transfer function for atom sphere color-coding and volume rendering. For volume rendering, this range clamps the atom energies before accumulation into the grid. If Max is not more than Min, it is defined as Min + 100. This clamp helps prevent outlier values from eliding information about the rest of the atoms in the molecule.
Visualized Energy Components
This group contains toggles for each partial energy component that is supported by the currently linked energy computation library. The partial energy of an atom is computed as the sum of those partial energy components whose toggle buttons are selected. Each atom's energy is taken as the sum of the terms selected in this box. Terms not selected do not make any contribution to the volume texture.

The Energy Rendering Dialog

This dialog, see Figure 6, is opened only from the Energy Visualization Dialog. To quickly see an energy texture, set the Visualize Energy toggle in the Energy Visualization Dialog and click the Generate Texture button in this dialog. Depending on the settings in the dialog, it might take anywhere from a fraction of a second to several minutes to generate the texture block. (The default settings are quick.) You may want to adjust the settings to make a better picture or make a picture faster. Also see the Guide to the Energy Visualization Pipeline for more information about the settings in this dialog as they pertain to energy rendering.



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Figure 6: The Energy Rendering Dialog.


Generate Texture
This button uses the AMBER energy for the molecule to generate a volume texture depicting the force field computed by the energy plug-in. Except for a minimization update or when loading a record, this button is the only way to update the energy texture after the molecule has changed.
Radius Multiplier
This slider controls the multiplier of the radial basis function in the pipeline.
Texels per Angstrom
This slider controls the resolution of the texture grid. Depending on the platform's capabilities and the buffer limit settings in the configuration file, the setting here may be replaced by a smaller value computed automatically.
Classifier
This choice determines the classifier function in the pipeline. This determines how many classifications are available for color function assignment in the group box below.
Color function
This choice assigns a color function to the selected classification in the pipeline. The intensity functions are usually best; the invisibility function can be used to hide parts of the texture.
Next Class
Go to the next classification for color function assignment.
Previous Class
Go to the previous classification for color function assignment.
Input Channel
These toggles select the input channel for the pipeline.
Radial Basis Function Coefficient Type
These toggles determine the coefficient type of the radial specifier in the pipeline.
Normalizing Interval
This group controls the pipeline's normalizing interval. If Calculate Automatically is selected, the normalizing interval will be computed by the pipeline to exactly match the range of the voxels, and the Min and Max fields will be disabled. If it is cleared, the Min and Max fields are enabled, allowing you to use the normalizing interval of a different force field than the current one, allowing comparison on the same visual scale.


You may want to use this feature in conjunction with other dialogs:

The Record Dialog

This dialog is invoked from the Energy Visualization Dialog by the Load Minimization Record button. With it you can interactively view the iteration steps of the minimization performed by the energy plug-in, if that feature is supported. One record is stored for each iteration, containing the energy values, atom positions, and force field gradients in the minimization state at the end of that iteration. A record file is compatible with a protein if it contains the same number of atoms as the protein and the same number of energy component terms as the current energy calculator plug-in. When a record file is loaded, the first record in the file is selected and applied to the protein in the main window.





File name
This field displays the name of the record file that was loaded, and how many records it contains.
Current record number
This field displays the selected record number. The single arrow buttons select the next or previous record. The double arrow buttons move to the first or last record in the file. The slider below allows arbitrary positioning; no effects are seen in the rest of the user interface until the mouse button is released from the slider.
Frame step
This is the number of iterations to include in each video frame, when the Generate Video Frames button is pressed. For example, if it is 20 (as shown), each frame will represent 20 iterations of the minimization, so for the file shown (161 records), there would be nine frames (eight each showing 20 iterations, and one showing only one).
Generate Video Frames
Beginning at the currently selected record, generate images from the main window to the end of the file. Frames are stored in PNG format for image quality; this feature requires that the ImageMagick toolkit be installed on your platform. The images are stored in a subdirectory called frames below the current working directory; any prior contents of the directory will be lost. The first frame shows only the current state of the protein at the time the button is pressed. Each subsequent record is loaded from the file and applied to the protein state (energy renderer, etc.). Every time a number of iterations equal to the frame step has been loaded, another frame is written to the file. The final frame may show fewer than the full number of iterations. Subsequent image processing and video encoding is beyond the scope of this application.


The BuildBeta Dialog

The BuildBeta Dialog, see Figure 7, is used to load a prediction file and PDB file for the BuildBeta routine as desribed in BuildBeta.




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Figure 7: The BuildBeta Dialog. (a) No prediction or PDB file is selected. (b) Both prediction and PDB files are selected.

Pred
This text field shows the loaded prediction file name.
PDB
This text field shows the loaded PDB file name.

You can load only a prediction file without a structure of a core part to perform the BuildBeta routine. Sometimes the structure of a core part of a protein is determined by homology with a known structure, and the task is to extend a sheet in the core by placing the remaining beta strands. In this case, both a prediction file and the corresponding PDB file with REMARK BEGINCORE and REMARK ENDCORE remarks should be loaded.