Force Field
Explorer
A Graphical User Interface to TINKER
June 2004, Version 4.2
Table of Contents
Description of Force Field Explorer
Components
Description of Force Field Explorer Menus
¨ Preferences
– Wireframe Thickness
¨ Apply
User Color to Selections
¨ Windows/Macintosh/Motif
Look & Feel
Force
Field Explorer is a graphical user interface to the TINKER suite of molecular
modeling tools. The goal is to create a robust environment for computational
chemistry and molecular engineering applications. Current features include:
·
Setup and real-time
visualization of modeling routines, including local/global optimizations,
sampling methods, superposition etc.
·
Basic 3D molecular
visualization (wireframe, spacefilling,
ball & stick, etc) with special features for force field specific
parameters such as Lennard-Jones radii and partial
charge magnitudes.
·
A comprehensive editor
for TINKER keyword files, which contain parameters that control modeling
algorithms.
·
TINKER trajectory playback.
This is the third release of Force Field Explorer, which is being labeled v. 4.2 and dated June 2004 to mirror the TINKER version it is compatible with. Dependencies, listed below, are now included in self-extracting installers for Linux, Mac OSX and Microsoft Windows.
1. TINKER version 4.2.
2. Java Runtime Environment (JRE) 1.4.X (1.4.2 preferred).
3. Java3D 1.3.X (1.3.1 preferred).
Major improvements over the 2nd release include:
· Self-Extracting Installers for Linux, Mac OSX (requires Panther 10.3) and Microsoft Windows. These distributions include TINKER binaries, source code, documentation, and example files. A JRE and Java3D libraries are included with the Linux and Windows installers. Mac OSX Panther 10.3 already includes a JRE, however Java3D must be obtained from the OSX website.
· An intuitive, consistent selection mechanism.
· Improved keyword and modeling panels.
· Support for TINKER internal coordinate, restart and induced dipole file formats, plus loading of Protein Databank files directly from the PDB or from disk. Conversion of PDB files to TINKER format (with automatic atom typing for many biomolecules) is also supported.
The most important Force Field
Explorer development goal is to add molecular editing features. We hope to soon
target JRE 1.5 "Tiger", and Java3D 1.4. Java3D has just been open
sourced by Sun, which has the potential to spur improvements to the API. Other
goals include a few more visualization methods and support for other file
types.
TINKER and Force Field Explorer
are now being distributed within self-extracting installers for Linux,
Macintosh OSX (Panther 10.3 and above) and Microsoft Windows. Included are binary TINKER executables, source code, example/test
files, documentation and the Java environment needed by Force Field Explorer
This is a private JRE that will not affect any other JREs
that may be installed system wide. The exception is Mac OSX, where only a
single System wide JRE is allowed.
For each
platform, a launch script/exe located in the top level installation directory
named “ffe” will launch Force Field Explorer.
On some
platforms, double clicking the ffe.jar file in the
“tinker/jar” directory will also launch Force Field Explorer. In this case,
your system JRE will be invoked instead of the private JRE in the install kit.
This is fine, as long as your system JRE is a 1.4.2 version that includes
Java3D 1.3.1 extensions.
After downloading the installer, execute it from a shell window. A script to run Force Field Explorer is located in the top level installation directory, which defaults to “/opt/TINKER”. In this case, TINKER binaries would be located in the “opt/TINKER/bin” directory. Any choice for installation directory is fine.
As mentioned above, Force Field Explorer only runs on Panther version 10.3 or later after installing the Macintosh Java3D implementation. It can be downloaded from the Macintosh OS X website:
http://www.apple.com/downloads/macosx/apple/java3dandjavaadvancedimagingupdate.html
After installing Java3D, download
“TINKER_macosx_4_2.sit”, and double click the file to un-stuff it. Then double
click the “Install TINKER and Force Field Explorer” icon to finish the
installation. A script to run Force Field Explorer is located in top level
TINKER directory while TINKER binaries are located in the “TINKER/bin”
directory.
After downloading the installer, double click to start installation. Force Field Explorer can then be launched from an icon or the Start Menu.
Description of Force Field Explorer
Components
The
Molecular Tree is a structural hierarchy of each system, used for navigating
and making selections. When Force Field Explorer opens a structure file, it
attempts to groups atoms into protein/nucleic acid macromolecules and their
constituent residues. It also groups ions, water and hetero molecules together.
This is done even in the absence of a TINKER sequence file. When a display or
color command is chosen, all currently selected groups of atoms are affected.
Figure 1. The
first residue of enkephalin has been selected in the
Tree view and is highlighted blue in the graphics window.
Left-clicking the Global Axis, then dragging performs a rotation about the origin of the entire scene. This is useful for manual docking of two systems. For example, after positioning each system individually in the X-Y plane by dragging them with the mouse, a rotation about the Y-axis allows orientation in the Y-Z plane. Right-clicking the Global Axis, then dragging performs a translation of the entire scene.
Figure 2.
Dragging the Graphics Axis causes the entire scene to rotate about the global
origin. The scene above has been rotated 180 degrees around the Y-axis.
The Keyword Editor allows modification of keyword files that control various aspects of TINKER calculations. If a Modeling Command is executed on a system, the corresponding Keyword File is automatically saved. Modifications can also be saved at any time using one of the save buttons. Any text or keywords that Force Field Explorer does not recognize are considered “Comments” and are appended to the end of saved key files. As an example, the enkephalin keyword control file is shown below.
Figure 3. The
Keyword Editor is displaying the enkephalin keyword
file.
The Modeling Commands panel of Force Field Explorer allows launching of most of the TINKER programs. After selecting a routine and configuring its modifying arguments, selecting the “play” button starts the job running. If TINKER will modify the coordinates of the system, Force Field Explorer will automatically connect to the routine and show progress interactively. If the routine completes before Force Field Explorer is exited, the textual results in the log file are loaded into the Logs panel. If Force Field Explorer exits while one or more routines are running, they continue in the background unless explicitly killed by the user. For example, the “Optimize” command has been selected for enkephalin (Figure 4).
Figure 4. The
OPTIMIZE routine has been selected in the Modeling Commands panel and will
execute on the active system, in this case enkephalin.
The Logs panel is a simple text editor where output logged from TINKER routines is automatically loaded. It can also be used to edit any text file, for example TINKER coordinate or keyword files.
Figure 5. The Log panel shows output logged from a TINKER Optimize command on enkephalin.
If a modeling command changes the coordinates of an open structure, the final structure generated is re-loaded onto the open structure used to initiate the command.
Figure 6. The coordinates for the local minima of enkephalin (enkephalin.xyz_2) were loaded onto the open structure (enkephalin.xyz) used to launch the TINKER optimize command.
Description of Force Field Explorer Menus
Force Field Explorer currently reads TINKER coordinate files (*.xyz, *.int), restart files (*.dyn),
archive files (*.arc), induced dipole files (*u) and Protein Databank files (*.pdb). However, file writing has only been implemented for
TINKER Cartesian coordinate files.
An attempt is made to open the
selected file. Currently, TINKER coordinate files, Archive files, and Protein
Databank files are recognized.
Saves the active file
under a different name. (This command is currently only supported for
Cartesian coordinate TINKER files)
Close the active file.
Close all open files.
Entering a valid 4 character accession will download the corresponding PDB file, save it to the current Force Field Explorer working directory, then open it.
TINKER Restart files (*.dyn) contain atomic positions, velocities and two sets of accelerations (current and previous step), but no connectivity information. Loading a Restart file on top of an open TINKER coordinate file allows visualization of velocities and accelerations.
TINKER Induced Dipole files (*.*u) contain induced dipole vectors. They are produced during a molecular dynamics routine using the TINKER “save-induced” keyword. Loading an Induced Dipole file on top of an open TINKER coordinate file allows visualization of induced dipoles.
Exit shuts Force Field Explorer down, saving user preferences.
The set of nodes currently
selected are highlighted in the Molecular Tree. If the shift key his pressed while
clicking on two nodes, all nodes in between are selected. Alternatively, by holding
down the control key while clicking on a node, either in the Tree or Graphics
window, the selection state of a node can be toggled. To use Graphics based
picking, the Graphics Picking checkbox under the Picking menu must be checked.
All open systems are selected.
Nodes that are not selected are made invisible.
Selected nodes are highlighted in the Graphics window.
Choose the color for selected atoms.
Selected atoms are labeled by number and description.
Selected residues are labeled by their respective three letter identifiers.
The default label size is 12 point.
The default font color is white.
We have intentionally maintained a
simple, but elegant rendering mechanism. The Force Field Explorer data
structure is self-rendering, meaning that each object “knows how to draw
itself”. Rendering commands are “Top-Down”, meaning that commands filter down
through the molecular tree, with each node responding and/or passing commands
to its children. This paradigm positions Force Field Explorer to easily scale
up to multi-level molecular engineering/nanotechnology modeling projects. What
we want to avoid is a rendering/data architecture built upon “an array of
atoms”. In our opinion, “an array of atoms” infrastructure can not achieve our
molecular engineering design goals. While a graphics change is being rendered,
one additional graphics command will be cached. Other commands are ignored
while the 3D view catches up. Changes are applied to all selected nodes in the Molecular
Tree View.
¨ Wireframe
Slow for large systems (more than a few thousand atoms).
¨ Spacefill
Slow for large systems (more than a
few thousand atoms).
Similar to Spacefill, but the sphere radii are set to the Lennard-Jones minima for the given atom.
Fill rendered polygons.
Render only vertices.
Render edges between vertices.
A scale factor applied to all rendered spheres and cylinders.
¨
Preferences – Wireframe Thickness
This specifies the thickness of wireframe representations in pixels.
Changes the number of vertices used in creating spheres and cylinders. More vertices (a higher number on the slider) create a smoother appearance, but slower rotations.
Black & White
rendering.
Atom based colors.
Color based on amino/nucleic acid.
Color based on secondary structure
specified in PDB files.
A different color is assigned to each polymer.
Coloring is based on partial charges that correspond to atom types specified in TINKER coordinate files.
Coloring is based on vector
magnitude, where the vector may represent velocity, acceleration, induced
dipole or force depending on user choice.
Arbitrary colors can be assigned to selected atoms by choosing the “Apply User Color to Selections” menu item. The “User Color” can then be selected to invoke this scheme.
¨ Apply User Color to Selections
See Above.
Specify the color to use when selecting the “Apply User Color to Selections” option.
Coordinate controls for the active
system.
· Reset Rotation
Removes any rotations applied to the active system.
· Reset Translation
Removes any translation applied to the active system.
· Reset Rotation and Translation
Removes any rotation/translation applied to the active system.
· Rotate About Center of Mass
Specifies the active system should be rotated about its center of mass.
· Reset About Pick
Specifies the active system should be rotated about the node selected by graphics picking.
Specify which system is controlled
by mouse clicking/dragging within the Graphics window.
· Active System
Regardless of mouse position, the Active system is controlled.
· System Below Mouse
To move a system, it must be
picked by clicking over it with the mouse.
Reset the global zoom that has been applied to the entire scene.
Remove any global translation that has been applied to the entire scene.
Remove any global rotation that has been applied to the entire scene.
Remove any global rotation and translation, then reset the global zoom.
¨ Toggle Hydrogens
Show/Hide hydrogen atoms.
Make the graphics window fill the entire screen.
Change the color of the graphics window background. This is useful for switching to a white background before capturing images that might be printed.
Graphics picking can be used to
select nodes anywhere in the structural hierarchy. By holding the control key
while picking, the selection state of the picked node is toggled between
selected/not selected. However, holding the shift button down
while picking currently has no effect.
Selecting this checkbox turns on Graphics Picking.
· Atom
Individual atoms will be picked.
· Bond
A Bond will be picked, with consecutive clicks cycling through all Bonds made by the picked atom.
· Angle
An Angle will be picked, with consecutive clicks cycling through all Angles made by the picked atom.
· Dihedral
A Dihedral will be picked, with consecutive clicks cycling through all Dihedrals made by the picked atom.
· Residue
· Polymer
· Molecule
· System
· Measure Distance
After selecting two atoms the distance between them will be reported in the Force Field Explorer console.
· Measure Angle
After selecting three atoms the angle formed between them will be reported in the Force Field Explorer console.
· Measure Dihedral
After selecting four atoms the dihedral formed between them will be reported in the Force Field Explorer console.
Picked nodes will be highlighted in the color selected using this control.
TINKER trajectories are stored in Archive files (*.arc), which are simply a concatenation of coordinate files (*.xyz, *.int).
When the end of a trajectory is reached, it is played in the reverse direction instead of restarting at the beginning.
Advance to an arbitrary frame of the active trajectory.
Choose a frame rate for trajectory playback. If 20 frames per second is entered, for example, a delay of 50 msec between coordinate changes is enforced. Therefore, the actual frame rate will be slower than what is specified if rendering for the system is slow.
Instead of displaying every frame during trajectory playback, only every nth frame will be rendered.
Play the active trajectory.
Stop the active trajectory.
Advance the active trajectory one frame.
Rewind the active trajectory one frame.
Return the active trajectory to the first frame.
TINKER sampling and optimization methods are configured to start a server that listens for Force Field Explorer clients. Once a client – server connection is made, simulation information can be sent between TINKER and Force Field Explorer. Multiple Force Field Explorer clients can connect to the same TINKER simulation.
If Force Field Explorer is connected to a TINKER simulation, the connection will be closed.
Force Field Explorer will attempt to connect to a TINKER simulation executing on the current computer.
Force Field Explorer will attempt to connect to a TINKER simulation executing on a remote computer.
Specify the IP address of the remote computer where a TINKER simulation is executing. No domain name server is used, so the address should be of the form: XXX.XXX.XXX.XXX
Currently, Force Field Explorer can save screenshots uses JPEG and PNG formats. More formats will be supported when we target Java 1.5 (this release targets Java 1.4.2). In most cases, PNG gives better image quality when using Force Field Explorer than JPEG, probably because the default JPEG configuration we are using chooses small image size over preservation of detail.
Capture the Graphics window to an image file.
Use the PNG image format.
Use the JPEG image format.
Force Field Explorer components can be customized to some extent to suit user preferences. Many user configurable choices are saved between sessions.
This resets the slider between the Molecular Tree and Graphics Windows to the default position. The Graphics window is a heavy weight component (so hardware graphics acceleration can be used), while most Force Field Explorer components are light weight “Swing” components. Unfortunately, this effect prevents the user from dragging the slider and shrinking the Graphics window.
Show/Hide the Tree view.
Show/Hide the Tool Bar.
Show/Hide the Global Axes. The Global Axes are used both as a visual cue and to affect global rotations and translations.
Show the command line Console.
This is the default appearance and should be consistent across platforms.
¨ Windows/Macintosh/Motif Look & Feel
This appearance should cause Force Field Explorer to more closely resemble the native platform.
This displays the TINKER logo and contact information.
Most of the work on Force Field Explorer has been done by me, Michael Schnieders, a 4th year graduate student with Jay Ponder. My undergraduate training was primarily in biochemistry and computer science. As a graduate student my focus has shifted to computational chemistry/molecular biology and statistical mechanics.
A significant contribution to Force Field Explorer was made by Zhiguang "Frank" Gao over the summer of 2002. The Force Field Explorer logo was provided by Pengyu Ren and shows an optimized AMEOBA gas phase water dimer. Special thanks go out to Alan Grossfield for offering many helpful suggestions. We would also like to thank Eric Reiss for making available his modified version of some Java3D Behaviors and Pat Niemeyer for his work in developing the BeanShell scripting framework. Needless to say, this tool (and the fun of creating it) exists due to the support of Jay Ponder.
I apologize for any bugs that
remain in Force Field Explorer. TINKER is known for its robustness and clean
code, and my goal is to achieve similar standards. Should you happen to perform
some command that causes a Java stack trace to be dumped to the console, please
copy the output and forward it to schnied@dasher.wustl.edu. Poor video card drivers can sometimes result in
unpredictable Force Field Explorer behavior. If this should happen, try to find
the latest drivers for your platform/video card combination.