Welcome!

Thank you for using TuftsViewer! Use the tabs below to select a tutorial.

Basics

Learn basics techniques for working with TuftsViewer.

Intermediate Techniques

Learn to use the sequence pane, residue pane, and top menu.

Multiple Alignment

Learn to use the multiple alignment feature.

The display pane is where the protein is visualized.

The sequence pane is the pane on the bottom of the window. Here multiple chains can be displayed.

The residue pane is on the right hand side of the window. Only one chain is displayed at at time here. The chain may be changed by using the drop down menu at the top of the pane.

To open a protein from web, go to the top menu and select "File">"Open Web...". A screen will appear where you can enter the 4 character pdb id. Tuftsviewer will locate the file and import it into the program, storing a copy of the pdb file locally.

To open a protein stored on your machine, go to the top menu and select "File">"Open". An explorer window will appear where you can navigate to the local pdb file.

To rotate the molecule, left-click and drag on it.

To zoom in and out, use the scroll wheel of the mouse. Alternatively, you may also hold both left and right mouse buttons down and move the mouse forward or backwards.

To pan hold the right mouse button and drag.

To reset the camera position, right-click on the display pane and select Reset Camera.

You can also reset zoom, and center the camera on the right-click menu.

There are multiple ways to select protein residues.

To select using the mouse, move the cursor over the residue you want to select, and left click on the model .

To deselect click on any portion of the black space in the protein model frame, or an empty part of the sequence pane. Note that deselection clears all selections made.

You may also select using a bounding box by holding shift and then left clicking and dragging.

To select a beta sheet or alpha helix, double click on a residue letter in the sequence pane, or on the portion in the model.

To select an entire chain in the display pane, triple click on the chain.

You may draw attention to certain areas by coloring protein residues, or restricting residues as seen in the model.

To accomplish these, first a portion of the protein must be selected.

To recolor, right click and select Pick Color....

To restrict the view, right click and select Hide All But Selected.

To uncolor all, right click and select "Color by Structure", or another coloring preset.

To unhide all, make sure you have nothing actively selected and under Display or the right-click menu select a model display type (Cartoon, etc.).

To show color in spacefill mode, make sure that on either the right click menu or the Display menu "Use Atom Colors" is deselected. Once that is done previously colored residues will be shown, and you also have the option to color by structure or alignment.

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TuftsViewer is an open source cross-platform protein structure viewer.

For more information, visit http://code.google.com/p/tuftsviewer/.

To select using the sequence pane click on a residue's letter.

To select multiple residues at one time you may click and drag.

When you mouse over a residue (either on the model, or over a letter) numbers are displayed on the bottom bar of the protein. Residue number is the second number from the right.

To select a beta sheet or alpha helix, double click on a residue letter in the structure.

To select a whole chain, left-click on the chain identifier (for example 1XYX: A).

Selections made in the sequence pane will update all panes.

Coloring, restricting, and changing the display view should be completed as they were in basic techniques.

To select using the residue pane click on the wanted residue.

To make a selection of contiguous residues, click on the first entry, then hold shift and then click on the last residue wanted.

To select disjoint residues, press control. Multiple sections can be selected by holding shift, then ctrl, then ctrl + shift.

Residue number is shown next to the residue identifier in the residue pane.

Selections made in the residue pane will update all panes.

Coloring, restricting, and changing the display view are completed as they were in basic techniques.

File

Save...: This feature allows a user to save their current work on a protein in TuftsViewer, a protein PDB file, or the protein's FASTA sequence.

Screenshot...: The screenshot option will allow you to save an image of just the display pane in multiple formats. It is possible to make high-resolution shots by adjusting the image resolution within this window.

Display

This menu is similar to the right click menu and can be used instead of right clicking.

Tools

Configuration...: This window has three panes: Colors, Paths, and Display.
        Colors: This pane is useful for changing the individual colors for default                   coloring schemes.
        Paths: This pane allows the user to change the location of cached pdb                   files and their default names.
        Display: This pane will be discussed in advanced options.

Windows

Use this menu to show/hide the residue and sequence panes.

Interface

This window will be discussed in advanced techniques.

Advanced Techniques

Parts of this section were taken from the Tuftsviewer wiki (courtesy of Matt Menke), located at the google code site that supports the source code.

Advanced Residue Selection

If "Xor Selection Rectangles" is selected in the Interface Menu, then when not pressing ctrl, the selection state of the residues in the selection rectangle is flipped. This means that dragging the selection rectangle over an area will deselect any selected residues and select any deselected residues.

Ctrl-A also serves to select all residues.

Ctrl-I inverts the current selection.

Settings Dialog

The Paths tab shows the locations of the local PDB and ASTRAL caches. If a local copy of either database already exists, just change the directory as needed to use it. Note that a number of file naming/location schemes are tried when searching for a local file (Compressed/uncompressed, single directory, or subdirectories using second and third letters of the PDB id, etc). In the URL, "%s" is replaced by the entire pdb or astral name, "%1" with the first character, "%2" with the second, etc. These codes do not work in the cache path fields.

The Display tab configures both how triangles are sent to OpenGL, the quality of the meshes that are used, the anti-aliasing level (if supported), and the dimensions of cartoons. Cartoon Quality is the number of slivers along the backbone while Cartoon Sliver Quality determines the number of triangles each sliver consists of. The cartoon for each residue uses roughly 8nm faces, where n is Cartoon Quality and m is Cartoon Sliver Quality. Spheres use roughly 12n^2 faces per sphere, where n is the Sphere Quality. Cylinders use 2n faces.

Interface Menu

The first set of options set the rotation mode. In all modes, dragging around the window's edges rotates the structure. In Arcball and Smoothed Arcball, the rotation is uniquely determined by where the left mouse button was pressed and where it's released. Also, after rotating and releasing the mouse, clicking and dragging back to the original location restore the original location. In Arcball, the angle of rotation per pixel the cursor is moved is lower near the center than the edges, while in Smoothed Arcball it's roughly constant throughout. Direct only considers the current cursor position, and the position it was the last time the cursor position was read, so where the cursor is relative to the window makes no difference, except around the edges of the window.

The next set of options set the rotation center. In Absolute mode, the model will always be rotated around the center of all atoms, regardless of whether or not they're visible or selection. In Visible mode, the center of all visible atoms, if any, is used. If none are visible, the Absolute center is used. In Selected Visible mode, the center of all visible selected atoms, if any, is used. If no selected atoms are visible, it acts just like Visible mode.

Double Click to Unselect allows greater control by requiring a double click to deselect any selected residues.

Multiple Alignment

The multiple alignment mode gives the user the ability to see how multiple protein chains are aligned. This can be viewed with the chains overlapping, side-by-side, or in separate windows.

To use multiple alignment, use to top menu to click "Tools", then "Multiple Alignment".

To add a chain to the alignment, click "Browse" in the "Run Alignment" window.

Find the first protein in your local pdb files and click "Open".

Now, click "Add" to include the protein in your alignment.

Repeat the last three steps until you have added as many chains as you need to the alignment.

To delete a chain from the alignment, click on the chain in the display window and click "Delete" at the bottom.

Choose a viewing style at the bottom of the window. Multiple frames in a single window will show the proteins side-by-side.

When you are satisfied, click "Ok".

Note that attempting to rotate, pan, zoom, color, or change the drawing style will complete the task for both chains.