:: DESCRIPTION
Chemitorium is Open-Source Molecule Editor and Viewer. Edit, compute, analyze and visualize chemical formulas. Formula Editor, 3D Rendering, Exporter, Video Module, Shaders, Antialiasing, Analysis Tools.
::DEVELOPER
Philipp Ruppel
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
N/A
:: DESCRIPTION
ViewMol3D is a 3D OpenGL viewer for molecular structures from the output of quantum chemistry calculations.
::DEVELOPER
Andrew Ryzhkov and Arcady Antipin
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
BlurLab simulate the full 3D light field of a fluorescence microscope, perform TIRF, FRAP or Z-slicing, add noise, and generate output images.It is an easy to use platform for generating simulated fluorescence microscopy data for use in mechanistic modeling visualization, image comparison, and hypothesis testing. The software accepts the 3D positions, intensities and labels of fluorescing objects that are produced by an underlying mechanistic model and transforms them into high quality simulated images. The program includes full 3D convolution with realistic (or even measured) point spread functions; inclusion of thermal, shot and custom noise spectra; simulations of mean and fully stochastic photobleacing; the ability to view scenes in wide-field and TIRF, and perform Z-slicing; and the ability simulate FRAP experiments.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
3MATRIX visualizes the three dimensional structure of eMATRIX motifs contained within structures from the Protein Structure Database (PDB). One needs the Chime plug-in to view the 3MATRIX motif structures. Multiple views of the structural motifs are possible.
::DEVELOPER
The Brutlag Bioinformatics Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Steven P. Bennett, Lin Lu, and Douglas L. Brutlag,
“3matrix and 3motif: A Protein Structure Visualization System for Conserved Sequence Motifs.”
Nucleic Acids Research.
:: DESCRIPTION
3MOTIF visualizes the three dimensional structure of eMOTIFs contained within structures from the Protein Structure Database (PDB). One needs the Chime plug-in to view the 3MOTIF structures. Multiple views of the structural motifs are possible.
::DEVELOPER
The Brutlag Bioinformatics Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Steven P. Bennett, Craig G. Nevill-Manning, and Douglas L. Brutlag, (2003)
“3motif: Visualizing Conserved Protein Sequence Motifs in the Protein Structure Database.”
Bioinformatics, Vol. 19 no. 4 2003, 541-542.
:: DESCRIPTION
VANO (Volume-object annotation system) is a System for 3D multicolor image stacks. VANO provides a well-coordinated way to annotate hundreds or thousands of 3D image objects. It combines 3D views of images and spread sheet neatly, and is just easy to manage 3D segmented image objects.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Peng, H., Long, F., Myers, E.W.,
“VANO: a volume-object image annotation system,”
Bioinformatics, Vol. 25, No. 5, pp. 695-697, 2009.
:: DESCRIPTION
CellExplorer is a package of computer programs to process and analyze 3D confocal image stacks of the model animal C. elegans, and can be applied to several other model systems such as fruit fly embryo/larvae as well. Some other applications include 3D cell/nuclei segmentation, quantification, gene expression analysis, automatic cell naming/annotation, cell targeting, etc.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Fuhui Long, Hanchuan Peng, Xiao Liu, Stuart Kim, and Eugene Myers,
“A 3D digital atlas of C. elegans and its application to single-cell analyses,”
Nature Methods, doi:10.1038/nmeth.1366, 2009.
:: DESCRIPTION
3D Chemical Elements Screensaver is the smartest interactive Periodic Table and 3D Atom Modelling software in the world. There is a great educational content with captivating info on each chemical element currently known by scientists. You can either let the screensaver entertain you or can easily control it with your mouse and keyboard.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
N/A
:: DESCRIPTION
top2maya is a script written in MEL (Maya Embedded Language) which runs in Alias|Wavefront’s Maya 2.5 and higher. It is a 3D visualization tool which analyzes images in 256 shades of gray and then displaces the individual pixels based on their color. It is a very effective tool for viewing 2D atomic force microscope images as 3D objects. As well as giving you a 3D image, it can also allow you to visualize multiple variables by doing the 3D displacement with one variable, for example the topography, then doing the shading on the new 3D object with another variable, for example surface friction.
::DEVELOPER
the Beckman Institute Imaging Technology Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
N/A
:: DESCRIPTION
PREPI (Protein REPresentations Interactively)is a molecular graphics program which can be used to EASILY produce and interactively manipulate many different types of molecular representations (cartoons) as well as providing quantative information on secondary structural topology. The program is not just limited to proteins, but can also show cartoon representations of NUCLEIC ACIDS. In fact the program is capable of displaying “ANY” object for which cartesian coordinates are available. The program can input data from a wide range of data file formats (e.g. Broohaven PDB, Cambridge Databank, SYBL, Z-MATRIX) including its own FREE FORMAT which allows for the construction of complex objects such as Virus particles.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
COPYRIGHT AGREEMENT FORM
You will need to sign and return this standard Copyright Agreement Form by email.
