DebiChem Project
Summary
3d visualization
DebiChem 3D Viewers

This metapackage will install 3D Viewers which might be useful for chemists.

Description

For a better overview of the project's availability as a Debian package, each head row has a color code according to this scheme:

If you discover a project which looks like a good candidate for DebiChem to you, or if you have prepared an unofficial Debian package, please do not hesitate to send a description of that project to the DebiChem mailing list

Links to other tasks

DebiChem 3d visualization packages

Official Debian packages with high relevance

Adun.app
Molecular Simulator for GNUstep (GUI)
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Adun is a biomolecular simulator that also includes data management and analysis capabilities. It was developed at the Computational Biophysics and Biochemistry Laboratory, a part of the Research Unit on Biomedical Informatics of the UPF.

This package contains UL, the Adun GUI frontend.

Please cite: Michael A. Johnston, Ignacio Fdez. Galván and Jordi Villà-Freixa: Framework-based design of a new all-purpose molecular simulation application: The Adun simulator. (PubMed) J. Comp. Chem. 26(15):1647-1659 (2005)
Registry entries: OMICtools 
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Avogadro
sistema de modelagem e gráficos moleculares
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Avogadro é um sistema de modelagem e gráficos moleculares para moléculas e biomoléculas. Pode visualizar propriedades como orbitais moleculares ou potenciais eletrostáticos e tem um construtor molecular intuitivo.

Inclui os seguintes recursos:

  • Modelador molecular com otimização automática de geometria baseada em campo de força;

  • Mecânica molecular incluindo restrições e buscas de confórmeros;

  • Visualização de orbitais moleculares e isosuperfícies gerais;
  • Visualização de vibrações e plotagem de espectro vibracional;
  • Suporte para células unitárias cristalográficas;
  • Geração de entrada para os pacotes de química quântica Gaussian, GAMESS e MOLPRO;

  • Arquitetura de extensões flexível e scripts em Python.

Os formatos de arquivos que o Avogadro pode ler incluem PDB, XYZ, CML, CIF, Molden, assim como a saída dos pacotes Gaussian, GAMESS e MOLPRO.

Please cite: Marcus D Hanwell, Donald E Curtis, David C Lonie, Tim Vandermeersch, Eva Zurek and Geoffrey R Hutchison: Avogadro: An advanced semantic chemical editor, visualization, and analysis platform. (eprint) J. Cheminf. 4:17 (2012)
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Ballview
ferramenta livre de modelagem e gráficos moleculares
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Visualização rápida baseada em OpenGL de estruturas moleculares, métodos de mecânica molecular (minimização, simulação MD usando os campos de força Amber, Charmm e MMFF94), cálculo e visualização de propriedades eletrostáticas (FDPB) e recursos de edição molecular.

Pode ser considerada uma interface gráfica de usuário construída sobre o Ball (Biochemical Algorithms Library, Biblioteca de Algoritmos Bioquímicos), com foco nas demandas mais comuns de químicos proteicos e biofísicos em particular. Foi desenvolvido nos grupos Hans-Peter Lenhof (Universidade Saarland, Saarbruecken, Alemanha) e Oliver Kohlbacher (Universidade de Tübingen, Alemanha). O Ball é uma infraestrutura em C++ especificamente projetada para desenvolvimento rápido de programas de modelagem molecular e Biologia molecular computacional. Fornece um conjunto amplo de estruturas de dados e classes para Mecânica molecular, métodos avançados de solvatação, comparação e análise de estruturas proteicas, importação/exportação de arquivos e visualização.

Please cite: Andreas Moll, Andreas Hildebrandt, Hans-Peter Lenhof and Oliver Kohlbacher: BALLView: a tool for research and education in molecular modeling. (PubMed,eprint) Bioinformatics 22(3):365-366 (2006)
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Cclib
Parsers and algorithms for computational chemistry
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A Python library that provides parsers for computational chemistry log files. It also provides a platform to implement algorithms in a package-independent manner.

This package contains helper scripts for end users.

If you are looking for the unit tests and data files managed by cclib, they are distributed separately as in non-free package cclib-data.

Please cite: Noel M. O'Boyle, Adam L. Tenderholt and Karol M. Langner: cclib: A library for package-independent computational chemistry algorithms. (eprint) J. Comp. Chem. 29(5):839-845 (2008)
Drawxtl
crystal structure viewer
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DRAWxtl reads a basic description of the crystal structure, which includes unit-cell parameters, space group, atomic coordinates, thermal parameters or a Fourier map, and outputs a geometry object that contains polyhedra, planes, lone-pair cones, spheres or ellipsoids, bonds, iso-surface Fourier contours and the unit-cell boundary.

Four forms of graphics are produced:

  • an OpenGL window for immediate viewing
  • the Persistence of Vision Ray Tracer (POV-RAY) scene language for publication-quality drawings
  • the Virtual Reality Modeling Language (VRML) for dissemination across the Internet
  • a Postscript rendering of the OpenGL window for those who want high-quality output but do not have POV-RAY installed.

File formats DRAWxtl can read include CIF, FDAT, FullProf (pcr), GSAS, SCHAKAL, SHELX, DISCUS and WIEN2k.

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Gabedit
graphical user interface to Ab Initio packages
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Gabedit is a graphical user interface to computational chemistry packages like:

  • MPQC
  • GAMESS-US
  • Gaussian
  • Molcas
  • Molpro
  • Q-Chem

These Ab Initio software packages might run locally or on a remote server (supporting FTP, RSH and SSH). Gabedit can display a variety of calculation results including most major molecular file formats. The advanced "Molecule Builder" allows one to rapidly sketch in molecules and examine them in 3D. Graphics can further be exported to various formats, including animations.

Please cite: Abdul-Rahman Allouche: Gabedit—A graphical user interface for computational chemistry softwares. (eprint) J. Comp. Chem. 32:174-182 (2011)
Gamgi
General Atomistic Modelling Graphic Interface (GAMGI)
Maintainer: Debichem Team
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The General Atomistic Modelling Graphic Interface (GAMGI) provides a graphical interface to build, view and analyze atomic structures. The program is aimed at the scientific community and provides a graphical interface to study atomic structures and to prepare images for presentations, and for teaching the atomic structure of matter.

The package is enhanced by the following packages: gamgi-data gamgi-doc
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Garlic
visualization program for biomolecules
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Garlic is written for the investigation of membrane proteins. It may be used to visualize other proteins, as well as some geometric objects. This version of garlic recognizes PDB format version 2.1. Garlic may also be used to analyze protein sequences.

It only depends on the X libraries, no other libraries are needed.

Features include:

  • The slab position and thickness are visible in a small window.
  • Atomic bonds as well as atoms are treated as independent drawable objects.
  • The atomic and bond colors depend on position. Five mapping modes are available (as for slab).
  • Capable to display stereo image.
  • Capable to display other geometric objects, like membrane.
  • Atomic information is available for atom covered by the mouse pointer. No click required, just move the mouse pointer over the structure!
  • Capable to load more than one structure.
  • Capable to draw Ramachandran plot, helical wheel, Venn diagram, averaged hydrophobicity and hydrophobic moment plot.
  • The command prompt is available at the bottom of the main window. It is able to display one error message and one command string.
Please cite: Damir Zucic and Davor Juretic: Precise Annotation of Transmembrane Segments with Garlic - a Free Molecular Visualization Program (eprint) Croatica Chemica Acta 77(1-2):397-401 (2004)
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Gausssum
parse and display Gaussian, GAMESS, and etc's output
Maintainer: Debichem Team
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GaussSum parses the output files of ADF, GAMESS, GAMESS-UK, Gaussian, Jaguar and PC GAMESS calculations to extract useful information.

GaussSum uses GNUPlot to display the progress of geometry optimisations, density of states spectrum, UV-VIS spectra, IR spectra, Raman spectra, and electron density difference maps. It can also display all lines containing an arbitrary phrase and more.

Please cite: Noel M. O'Boyle, Adam L. Tenderholt and Karol M. Langner: cclib: A library for package-independent computational chemistry algorithms. J. Comp. Chem. 29(5):839-845 (2008)
Gdis
molecular and crystal model viewer
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A GTK+ based program for the display and manipulation of isolated molecules, periodic systems and crystalline habits. It is in development, but is nonetheless fairly functional. It has the following features:

  • Support for several file types (CIF, BIOSYM, XYZ, XTL, MARVIN, and GULP)
  • A simple molecular creation and manipulation tool
  • A dialogue for creating starting configurations for molecular dynamics simulations
  • Assorted tools for visualization (geometry information, region highlighting, etc.)
  • Animation of BIOSYM files (also rendered animations, see below)

GDIS also allows you to perform the following functions through other packages:

  • Model rendering (courtesy of POVRay)
  • Energy minimization (courtesy of GULP)
  • Morphology calculation (courtesy of cdd)
  • Space group processing (courtesy of SgInfo)
  • View the Periodic Table (courtesy of GPeriodic)
  • Load additional filetypes, such as PDB (courtesy of Babel)
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Gdpc
visualizador de simulações moleculares dinâmicas
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O gpdc é um programa gráfico para visualização de dados de saída a partir de simulações da dinâmica molecular. Ele lê dados de entrada no formato padrão xyz, assim como outros formatos personalizados, e pode gerar imagens de cada quadro nos formatos JPG ou PNG.

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Jmol
visualizador molecular
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Jmol é um visualizador molecular desenvolvido em Java para estruturas químicas tridimensionais. Seus recursos incluem a leitura de uma variedade de tipos de arquivos, a saída de programas de química quântica, animação de arquivos multi-quadro e modos normais calculados a partir de programas quânticos. Inclui recursos para produtos químicos, cristais, materiais e biomoléculas. Jmol pode ser útil para estudantes, professores e pesquisadores em química e bioquímica.

Os formatos de arquivos lidos pelo Jmol incluem PDB, XYZ, CIF, CML, MDL Molfile, Gaussian, GAMESS, MOPAC, ABINIT, ACES-II, Dalton e VASP.

Please cite: A. Herráez: Biomolecules in the computer: Jmol to the rescue. (PubMed,eprint) Biochem Mol Biol Educ. 34(4):255-261 (2006)
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Kalzium
periodic table and chemistry tools
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Kalzium is a full-featured chemistry application, including a Periodic Table of Elements, chemical reference, chemical equation solver, and 3D molecule viewer.

This package is part of the KDE education module.

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P4vasp
visualization suite for the Vienna Ab-initio Simulation Package (VASP)
Maintainer: Debichem Team
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p4VASP is a visualization suite for the Vienna Ab-initio Simulation Package (VASP). It contains an extensible GUI framework, that can be used to view material structure, density of states, band-structure and more.

It provides a Python library, that greatly simplifies the process of manipulation of the VASP input and output data in Python scripts. P4vasp utilizes also many handy routines and objects e.g. for creating 2D graphs, data storage (xml,DOM) or simple matrix library.

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Qutemol
Visualização interativa de macromoléculas
Maintainer: Debichem Team
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QuteMol é um sistema visualizador molecular interativo de alta-qualidade. Ele explora a capacidade atual da GPU através de sombreamento OpenGL para oferecer uma variedade de efeitos visuais inovadores. As técnicas de visualização do QuteMol visam clareza e uma compreensão mais fácil da forma (shape) 3D e estrutura de moléculas grandes ou proteínas complexas.

Qutemol usa técnicas avançadas do OpenGL e pode não funcionar corretamente com todas as placas de vídeos e drivers.

Recursos inclusos no QuteMol:

  • Oclusão de ambiente em tempo real
  • Melhoria da silhueta ciente da profundidade
  • Modos de visualização de modelos de bolas e varetas, preenchimento de espaço (space-filling) e alcaçuz (liquorice)

  • Foto de tela (snapshot) de alta resolução suavizados para criação de publicações renderizadas com qualidade

  • Geração automática de gifs animados de moléculas girando para animações de páginas web

  • Renderização interativa de macromoléculas (> 100 mil átomos)

QuteMol lê arquivos PDB como entrada.

Please cite: Marco Tarini, Paolo Cignoni and Claudio Montani: Ambient Occlusion and Edge Cueing for Enhancing Real Time Molecular Visualization. (eprint) IEEE Transactions on Visualization and Computer Graphics 12(5):1237-1244 (2006)
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Rasmol
visualization of biological macromolecules
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RasMol is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images.

The program reads in a molecule coordinate file and interactively displays the molecule on the screen in a variety of colour schemes and molecule representations. Currently available representations include depth-cued wireframes, 'Dreiding' sticks, spacefilling (CPK) spheres, ball and stick, solid and strand biomolecular ribbons, atom labels and dot surfaces.

Supported input file formats include Protein Data Bank (PDB), Tripos Associates' Alchemy and Sybyl Mol2 formats, Molecular Design Limited's (MDL) Mol file format, Minnesota Supercomputer Center's (MSC) XYZ (XMol) format, CHARMm format, CIF format and mmCIF format files.

This package installs two versions of RasMol, rasmol-gtk has a modern GTK-based user interface and rasmol-classic is the version with the old Xlib GUI.

The package is enhanced by the following packages: rasmol-doc
Please register by following this link if you are using rasmol.
Please cite: Roger A. Sayle and E. James Milner-White: RasMol: Biomolecular graphics for all. (PubMed) Trends in Biochemical Sciences (TIBS) 20(9):374 (1995)
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Raster3d
tools for generating images of proteins or other molecules
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Raster3D is a set of tools for generating high quality raster images of proteins or other molecules. The core program renders spheres, triangles, cylinders, and quadric surfaces with specular highlighting, Phong shading, and shadowing. It uses an efficient software Z-buffer algorithm which is independent of any graphics hardware. Ancillary programs process atomic coordinates from PDB files into rendering descriptions for pictures composed of ribbons, space-filling atoms, bonds, ball+stick, etc. Raster3D can also be used to render pictures composed in other programs such as Molscript in glorious 3D with highlights, shadowing, etc. Output is to pixel image files with 24 bits of color information per pixel.

Please cite: E.A. Merritt and D.J. Bacon: Raster3D Photorealistic Molecular Graphics. (PubMed) Methods in Enzymology 277:505-524 (1997)
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Shelxle
graphical user interface for SHELXL
Maintainer: Debichem Team
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ShelXle combines an editor with syntax highlighting for the SHELXL-associated .ins (input) and .res (output) files with an interactive graphical display for visualization of a three-dimensional structure including the electron density (Fo) and difference density (Fo-Fc) maps.

http://dx.doi.org/10.1107/S0021889811043202

Please cite: Christian B. Hübschle, George M. Sheldrick and Birger Dittrich: ShelXle: a Qt graphical user interface for SHELXL. (eprint) J. Appl. Cryst. 44(6):1281-1284 (2011)
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V-sim
Visualize atomic structures
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V_Sim visualizes atomic structures such as crystals, grain boundaries, molecules and so on (either in binary format, or in plain text format).

The rendering is done in pseudo-3D with spheres (atoms) or arrows (spins). The user can interact through many functions to choose the view, set the bindings, draw cutting planes, compute surfaces from scalar fields, duplicate nodes, measure geometry... Moreover V_Sim allows one to export the view as images in PNG, JPG, PDF (bitmap), SVG (scheme) and other formats. Some tools are also available to colorize atoms from data values or to animate on screen many position files.

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Viewmol
graphical front end for computational chemistry programs
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Viewmol is able to graphically aid in the generation of molecular structures for computations and to visualize their results.

At present Viewmol includes input filters for Discover, DMol3, Gamess, Gaussian 9x/03, Gulp, Mopac, PQS, Turbomole, and Vamp outputs as well as for PDB files. Structures can be saved as Accelrys' car-files, MDL files, and Turbomole coordinate files. Viewmol can generate input files for Gaussian 9x/03. Viewmol's file format has been added to OpenBabel so that OpenBabel can serve as an input as well as an output filter for coordinates.

Registry entries: SciCrunch  OMICtools 
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Xbs
modelos e filmes 3-d de moléculas
Maintainer: Matthew Vernon
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O programa xbs de desenho tipo bolas-e-varetas pode criar modelos de moléculas tridimensionais, parados e em movimento. Estão disponíveis saídas X11 e PostScript. Os modelos podem ser rotacionados, ter a escala alterada, etc. Várias opções de rótulos, sombras, luzes e cores estão disponíveis.

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Xcrysden
visualizador de estrutura molecular e cristalina
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XCrySDen é um programa de visualização de estrutura molecular e cristalina que tem o objetivo de exibir isosuperfícies e contornos, que podem ser sobrepostos em estruturas cristalinas e interativamente rotacionadas e manipuladas. Ele pode ser executado na maioria das plataformas UNIX sem quaisquer requisitos especiais de hardware.

XCrySDen permite a captura em tempo real de exibição. Vários codificadores de filme são suportados, em particular são necessários para conversão de GIF animado (imagemagick), gifsicle ou whirlgif. É necessário para AVI/MPEG mencoder ou ppmtompeg (netpbm). Precisa estar presente para a janela de *dumps", imagemagick ou xwd (x11-apps).

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Xmakemol
program for visualizing atomic and molecular systems
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XMakemol is a mouse-based program, written using the LessTif widget set, for viewing and manipulating atomic and other chemical systems. It reads XYZ input and renders atoms, bonds and hydrogen bonds.

Features include:

  • Animating multiple frame files
  • Interactive measurement of bond lengths, bond angles and torsion angles
  • Control over atom/bond sizes
  • Exporting to Xpm, Encapsulated PostScript and XYZ formats
  • Toggling the visibility of groups of atoms
  • Editing the positions of subsets of atoms
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