Software Tools For Molecular Microscopy/Visualization and modeling tools

ADP_EM http://chaconlab.org/adpem/index.html ADP_EM is an ultra fast multiresolution fitting tool of atomic structures into low/medium resolution EM maps which has been specially designed to support high throughput coverage. The method uses spherical harmonics to effectively speed up the rotational scan. It can be considered as a practical step-down of the Fast Rotational Matching (FRM) described elsewhere in Kovacs et al. 2003. Please, download the program and test by yourself the efficiency and robustness reached with this new approach. 1.03 pablo@chaconlab.org Windows, Linux CCP4, SITUS Free C/C++ J.I. Garzón Julio A. Kovacs; Ruben Abagyan; and P. Chacón. 2007 ADP_EM: Fast exhaustive multi-resolution docking for high-throughput coverage. Bioinformatics 23 4 427-33 Julio A. Kovacs, Pablo Chacón, Yao Cong, Essam Metwally, and Willy Wriggers Fast Rotational Matching of Rigid Bodies by Fast Fourier Transform Acceleration of Five Degrees of Freedom. Acta Cryst. D. 59 1371-1376 2003 Amira http://www.amira.com Amira is a software solution that satisfies your demanding needs to work with clinical or preclinical image data, nuclear data, optical or electron microscopy imagery, molecular models, vector and flow data, simulation data on finite element models, and all types of multidimensional image, vector, tensor, and geometry data. 5.4.3. info@vsg3d.com Win/Linux/Mac TIFF, BMP, JPEG, PNG, SGI, Leica, Zeiss, BioRad, Olympus, MRC, DICOM, Analyze 3D, Fidap, I-DEAS, Fluent, DXF, STL, VRML, Inventor, CATIA 4/5, IGES Depends on license Stalling Detlev Malte Westerhoff, Hans-Christian Hege Charles D. Hansen Christopher R. Johnson The Visualization Handbook Elsevier 2005 749-767 Chapter 38, Amira: A Highly Interactive System for Visual Data Analysis http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.129.6785&rep=rep1&type=pdf Automated Segmentation of Actin Networks (Software Package for Amira) http://www.zib.de/en/visual/software/cryoem.html This software package brings an automated procedure for the segmentation of actin filaments from cryo-electron tomograms. It is based on a combination of template matching with a new tracing algorithm and allows a statistically sound assessment of the properties of filamentous actin networks. The whole analysis workflow, from denoising to segmentation, can be performed within the visualization framework Amira 5.4.5 Our segmentation package enables the user to obtain geometric data on individual actin filaments and to use this data for statistical analysis. The software has been developed in collaboration between the Zuse Institute Berlin (ZIB) and the Max Planck Institute of Biochemistry. 1.4 baum at zib dot de / rigort at biochem dot mpg dot de 64-bit versions for Linux and Windows, 32-bit version for MacX. 3D tomographic data, EM, MRC, others package: free for academic use; Amira trial license (valid for 3 weeks) available, otherwise: licensed version of Amira 5.4.5 required Rigort A., Guenther D., Hegerl R., Baum D., Weber B., Prohaska S., Medalia O., Baumeister W., Hege H.C Automated segmentation of electron tomograms for a quantitative description of actin filament networks http://www.ncbi.nlm.nih.gov/pubmed/21907807 J. Struct. Biol. 21907807 10.1016/j.jsb.2011.08.012 CoAn/CoFi http://coan.burnham.org Software for statistics-based fitting of atomic models into density maps of lower resolution such as those obtained by electron microscopy and image reconstruction. coan@burnham.org Linux MRC Free for academic users Volkmann N, Hanein D 1999 Quantitative fitting of atomic models into observed densities derived by electron microscopy J. Struct. Biol. 125 176-184 10222273 Volkmann N, Hanein D 2003 Docking of atomic models into reconstructions from electron microscopy Methods Enzymol. 374 204-225 14696375 Volkmann N 2009 Confidence intervals for fitting of atomic models into low-resolution densities Acta Crystallogr D Biol Crystallogr. 65 679-689 19564688 UCSF Chimera http://www.cgl.ucsf.edu/chimera Molecular modeling package with many density map capabilities. Supports fitting atomic models in maps, interactive segmentation, coarse modeling, measuring and coloring of density maps for elucidating structures of large molecular assemblies. The map capabilities were designed for analyzing electron microscope single particle reconstructions and tomography. Includes many methods for analysis of atomic resolution molecular models and multiple sequence alignments. 1.4.1 chimera-users@cgl.ucsf.edu Windows, Macintosh, Linux MRC, CCP4, SPIDER, BRIX, SITUS, PIF, HDF5, others Free for academic use TD Goddard Huang CC, Ferrin TE 2007 Visualizing density maps with UCSF Chimera Journal of Structural Biology 157 1 281-7 16963278 coloRNA http://franklab.cpmc.columbia.edu/franklab/colorna The purpose of coloRNA is the following: if we have two versions of an RNA structure (given as pdb files), differing as a consequence of conformational changes, and given the secondary structure, then the program is able to determine the distances between corresponding residues and heat-map them onto the secondary structure.  That is, very mobile/flexible residues show up in red, moderate ones in yellow and green, very stable ones in blue. So it is possible, with the aid of the program, to determine which parts of the secondary structure are responsible for the mobility of the 3D structure. 1.1 hl2485@columbia.edu Linux pdb files, others file formats (see readme.txt) Free Python 2.3.3 with Tkinter 8.4 J. LeBarron Mitra, K., and Frank, J. 2007 Displaying 3D data on RNA secondary structures: coloRNA. J Struct Biol 157 1 262-270 17070699 10.1016/j.jsb.2006.08.018 EMDataBank http://www.emdatabank.org EMDataBank.org, a resource for deposition and retrieval of 3DEM map, model and associated metadata, unifies public access to the two major EM Structural Data archives: EM Data Bank (EMDB) and Protein Data Bank (PDB), and facilitates use of EM structural data by the wider scientific community. The resource offers Java-based 3D viewers which can be accessed from EMDataBank atlas pages. Atlas pages of interest can be found using EMSEARCH (http://www.emdatabank.org/search.html). AstexViewer, a molecular graphics program originally developed to display crystallographic data was recently re-released under an open source license and has been adapted for display of EM maps and associated PDB coordinate models. A compact map format is used to improve web download speed and minimize memory requirements (very large maps are down-sampled). Current capabilities include ability to control map contour level, opacity, color, solid vs. mesh surface rendering, and concurrent display of one or more PDB coordinate entries. help@emdatabank.org requires web browser with Java (1.5 or higher preferred), viewing large maps may require increasing the Java Runtime memory Free C. Lawson et al. 2011 EMDataBank.org: Unified Data Resource for Cryo EM Nucleic Acids Research 39(Database issue) D456 20935055 10.1093/nar/gkq880 PMC3013769 M. Tagari et al. 2002 New electron microscopy database and deposition system Trends Biochem. Sci. 27 589 12417136 K. Henrick et al. 2003 EMDep: a web-based system for the deposition and validation of high-resolution electron microscopy macromolecular structural information J. Struct. Biol. 144 228 14643225 EMfit http://bilbo.bio.purdue.edu/~viruswww/Rossmann_home/softwares/emfit.php Program for fitting atomic models into electron microscopy maps. Fitting criteria includes the sum of densities at atomic sites, the lack of atoms in negative or low density, the absence of atomic clashes between symmetry-related positions of the atomic structure, and the distances between identifiable features in the map and their positions on the fitted atomic structure, etc. 5.0 mr@indiana.bio.purdue.edu Linux, AIX TSB ASCII EM, XPLOR ASCII Free/Open Source M.G. Rossmann R. Bernal, S. V. Pletnev 2001 Combining electron microscopic with X ray crystallographic structures Journal of Structural Biology 136 190-200 M.G. Rossmann 2000 Fitting atomic models into electron microscopy maps Acta Crystallogr D56 1341-1349 EMPackage (Electron Tomography Toolbox for Amira) http://www.biophys.uni-frankfurt.de/frangakis/Amiratools.htm The EMPackage is a powerful toolbox for three-dimensional electron microscopy in Amira. The main aim of the toolbox is to decrease the amount of different programs needed to analyse EM data, by enabling denoising and segmentation tasks directly in Amira. Amira has to be installed and a license is needed for Amira. 1.0.0 frangakis.group@googlemail.com Win/Linux/Mac File formats supported in Amira plus additionally CCP4, EM, IMAGIC, SPIDER Free for academic use, but requires Amira S. Pruggnaller M. Mayr, A.S. Frangakis 2008 A visualization and segmentation toolbox for electron microscopy Journal of Structural Biology Gorgon http://gorgon.wustl.edu An interactive molecular modeling system specifically geared towards cryo-EM and other low resolution structures of macromolecular complexes. The long term goal of the gorgon project is to be able to address to every part of the molecular modeling pipeline starting from the initial volumetric reconstruction of the complex all the way to the final placement of each individual atom. Gorgon is being developed as a collaboration between Washington University in St. Louis and Baylor College of Medicine. Gorgon currently provides the following feature categories: Visualization: A comprehensive visualization framework for volumetric data (iso-contours, cross-sections and solid rendering), geometric skeletons, secondary structure elements and atomic models (PDB). Geometric operations: Many geometric operations such as skeletonization (binary / grayscale and interactive), smoothing, resampling, cropping, etc. are provided. Protein structure prediction: We provide tools which allow users to find the correspondence between predicted secondary structure elements in the sequence and the observed secondary structure elements in the volume Protein backbone tracing: The c-alpha backbone of a protein can be easily traced manually or semi-automatically using the many supporting elements offered by Gorgon. 2.0.0 sasakthi.abeysinghe@wustl.edu Windows 2000/XP/Vista, MacOS X, Linux MRC, CCP4, RAW, OFF, PDB, SEQ, SSE, WRL/VRML Free S.S. Abeysinghe Baker, M., Chiu, W., and Ju, T. 2008 Segmentation-free skeletonization of grayscale volumes for shape understanding Shape Modeling and Applications 63-71 S.S. Abeysinghe Ju, T., Baker, M., and Chiu, W. 2008 Shape modeling and matching in identifying 3D protein structures Computer-Aided Design 40 6 708-720 M. Baker Ju, T., and Chiu, W. 2007 Identification of Secondary Structure Elements in Intermediate Resolution Density Maps Structure 15 1 7-19 T. Ju Baker, M., and Chiu, W. 2007 Computing a family of skeletons of volumetric models for shape description Computer-Aided Design 39 5 352-360 IMOD see Software_Tools_For_Molecular_Microscopy/Specific_packages#IMOD iMODFIT http://chaconlab.org/imodfit/index.html iMODFIT is an efficient tool for fast flexible fitting of atomic structures into low/medium resolution EM maps based on Normal Mode Analysis in internal Coordinates. It is able to deal with protein and nucleic acid structures with small ligands at several coarse-graining levels. Please, download the program and test by yourself the efficiency and robustness reached with this new approach. 1.02 pablo@chaconlab.org Linux CCP4, SITUS Free C/C++ J.R. López-Blanco Garzón, J.I. ; Chacón, P. 2011 (in preparation) NORMA http://www.elnemo.org/NORMA NORMA is a freely available software suite that allows the modelling of large conformational changes of high-resolution three-dimensional protein structures under the constraint of a low-resolution electron-density map. Typical applications are the interpretation of electron-microscopy data using atomic scale X-ray structural models. The software package provided should enable the interested user to perform flexible fitting on new cases without encountering major technical difficulties. The NORMA software suite includes three fully executable reference cases and extensive user instructions. It comes with a Linux version of the URO fitting package (by J. Navaza) and the elNemo elastic network model normal mode analysis code (by Y.H. Sanejouand). 1.0 Karsten Suhre Linux EZD, CCP4, MRC, PIF Free K. Suhre Navaza, J., and Sanejouand, Y.H. 2006 NORMA: a tool for flexible fitting of high resolution protein structures into low resolution electron microscopy derived density maps Acta Cryst D62 1098-1100 OpenStructure http://www.openstructure.org OpenStructure is a software development platform tailored to the implementation of novel computational structural biology and molecular modeling methods. OpenStructure has been designed to handle and manipulate a wide range of data types as required in the field of integrative modeling, where data originating from a variety of experimental techniques are used to guide the model building process. The toolkit allows the development of sophisticated stand-alone applications, but also offers interfaces to flexibly incorporate external software, where appropriate, without the need to re-implement existing functionalities. At the top level, OpenStructure features a graphical user interface with components for rendering of biological macromolecules, density maps, image stacks, widgets for sequence analysis and graphical scene setup, and an integrated Python shell. While the graphical interface is conveniently used without prior knowledge of the underlying layers, the GUI maintains a tight integration with the scripting functionality. Any object that is visualized on the screen can be accessed at the Python level. Likewise, it is possible to create and manipulate graphical objects from within a script. This setup allows the combination of human-based and automatic data analysis, and freely customizing the graphical interface itself. 1.0.0 Torsten Schwede Win/Linux/MacOS X CCP4, DAT, TIFF, MRC, SPIDER, Nanoscope, PNG, SITUS, JPK, PDB, SDF, CRD, CHARMM trajectory files, maestro, many sequence and alignment formats Free LGPL C++/Python M. Biasini Mariani V., Haas J., Scheuber S., Schenk A.D., Schwede T., and Philippsen A. 2010 OpenStructure: a flexible software framework for computational structural biology Bioinformatics 26 20 2626–2628 20733063 10.1093/bioinformatics/btq481 PMC2951092 PyMOL http://pymol.org 1.2 licensing@schrodinger.com Linux, Unix, Mac OS X, and Windows CCP4, MRC, PDB, many more Subscription/Open Source Python Unpublished RIVEM http://bilbo.bio.purdue.edu/~viruswww/Rossmann_home/softwares/river_programs/rivem.php Program developed to project electron density of virus radially onto a sphere that is then presented as a stereographic diagram. Features that constitute the viral surface can be simultaneously represented in terms of atoms, amino acid residues, potential charge distribution, and surface topology 3.2 xc@purdue.edu Linux, AIX XPLOR ASCII Free C. Xiao Rossmann, M. G. 2007 Interpretation of electron density with stereographic roadmap projections Journal of Structural Biology 158 182-187 Sculptor http://sculptor.biomachina.org/ Sculptor is an interactive multi-resolution docking and visualization program for low-resolution density maps and atomic structures. We are developing Sculptor as a GUI-based extension of the Situs docking programs, to allow an interactive exploration and analysis of volumetric maps. Sculptor combines 3D rendering with advanced mathematical concepts like clustering techniques and pattern matching algorithms to permit an almost instantaneous fitting of the high-resolution structures and to facilitate typical post-processing work like map editing or resolution adjustment. 2.1 sculptor@biomachina.org Windows, Macintosh, Linux MRC, CCP4, SITUS, SPIDER Free/Open Source LGPL C++ S. Birmanns Rusu M, Wriggers W 2011 Using Sculptor and Situs for Simultaneous Assembly of Atomic Components into Low-Resolution Shapes J. Struct. Biol. 10.1016/j.jsb.2010.11.002 Heyd J, Birmanns S Immersive Structural Biology: A New Approach to Hybrid Modeling of Macromolecular Assemblies Virtual Reality 13 245-255 2009 July Rusu M, Birmanns S, Wriggers W Biomolecular pleiomorphism probed by spatial interpolation of coarse models Bioinformatics 24 21 2460–6 2008 November 18757874 2732278 10.1093/bioinformatics/btn461 Birmanns S, Wriggers W Interactive Fitting Augmented by Force-Feedback and Virtual Reality J Struct Biol 144 123-131 2003 Situs http://situs.biomachina.org/ Situs is a modular software package for the integration of biophysical data across the spatial resolution scales. It has been developed over the last decade with a focus on bridging the resolution gap between atomic structures, coarse-grained models, and volumetric data from low-resolution biophysical origins, such as electron microscopy, tomography, or small-angle scattering. Structural models can be created and refined with various flexible and rigid body docking strategies. The software consists of multiple, stand-alone programs for the format conversion, analysis, visualization, manipulation, and assembly of 3D data sets. 2.7 situs@biomachina.org Windows, Macintosh, Linux MRC, CCP4, SITUS, SPIDER, XPLOR, ASCII Free/Open Source GPL C/C++ W. Wriggers 2010 Using Situs for the Integration of Multi-Resolution Structures Biophysical Reviews 2 21-27 20174447 10.1007/s12551-009-0026-3 PMC2821521 Wriggers W, Chacón P Modeling tricks and fitting techniques for multiresolution structures Structure 9 9 779–88 2001 September 11566128 Chacón P, Wriggers W Multi-resolution contour-based fitting of macromolecular structures J. Mol. Biol. 317 3 375–84 2002 March 11922671 10.1006/jmbi.2002.5438 Rusu M, Birmanns S, Wriggers W Biomolecular pleiomorphism probed by spatial interpolation of coarse models Bioinformatics 24 21 2460–6 2008 November 18757874 2732278 10.1093/bioinformatics/btn461 UROX http://sites.google.com/site/xsiebert/urox An interactive tool for fitting atomic models into electron microscopy reconstructions (or into envelopes derived from small-angle X-ray or neutron scattering). The correlation between the electron density of the atomic models and the map is calculated and updated as a model is moved on the graphical display with the help of the mouse. Calculations are performed in reciprocal-space and the symmetry of the reconstruction is taken into account. The computations are fast and an entire EM reconstruction can be used. Versions above 2.0 include Normal-Modes flexible fitting and "map on map" fitting (in addition to "model in map" fitting). 2.0.2 xsiebert@gmail.com Linux EZD, CCP4, MRC, PIF Free Siebert X, Navaza J UROX 2.0: an interactive tool for fitting atomic models into electron-microscopy reconstructions Acta Crystallogr. D Biol. Crystallogr. 65 Pt 7 651–8 2009 July 19564685 2703571 10.1107/S0907444909008671 Navaza J, Lepault J, Rey FA, Alvarez-Rúa C, Borge J On the fitting of model electron densities into EM reconstructions: a reciprocal-space formulation Acta Crystallogr. D Biol. Crystallogr. 58 Pt 10 Pt 2 1820–5 2002 October 12351826 V3D http://penglab.janelia.org/proj/v3d V3D is a general tool for 3D microscopy image visualization and analysis, as well as display and analysis of the extracted surface models. It features fast 3D rendering of large data sets. It comes with a flexible plugin interface which allows developing additional toolkits easily. V3D is cross-platform and runs on Mac, Linux and Windows. It has a number of easy to use features specially designed for multicolor 3D microscopic data. 2.687 pengh@janelia.hhmi.org Mac, Linux, and Windows tif, LSM, RAW, MRC Free H. Peng et al. 2010 V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets Nature Biotechnology 28 4 348-353 10.1038/nbt.1612