DebiChem Project
Summary
3D Visualization
DebiChem - przeglądarki 3D

Ten metapakiet instaluje przeglądarki 3D, które mogą być przydatne dla chemików.

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
Symulator molekularny do GNUstep-a (GUI)
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Adun jest symulatorem biomolekularnym, który umożliwia także zarządzanie danymi i ich analizę. Został stworzony przez Computational Biophysics and Biochemistry Laboratory (laboratorium obliczeń biofizycznych i biomedycznych), będące częścią Research Unit on Biomedical Informatics (jednostki badawczej nad informatyką biomedyczną) na UPF.

Pakiet zawiera UL, frontend z graficznym interfejsem użytkownika do symulatora Adun.

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)
Screenshots of package adun.app
avogadro
System do molekularnego modelowania i wizualizacji
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Avogadro jest systemem do molekularnego modelowania oraz wizualizacji cząsteczek i biocząsteczek. Może wizualizować właściwości cząsteczek, takie jak orbitale lub potencjały elektrostatyczne, a ponadto udostępnia intuicyjne narzędzie do budowania cząsteczek.

Podstawowe możliwości:

  • molekularne modelowanie z automatyczną optymalizacją opartą na geometrii pól siłowych;
  • mechanika molekularna obejmująca wyszukiwanie według ograniczeń i konformacji;
  • wizualizacja orbitali molekularnych oraz ogólnych izopowierzchni;
  • wizualizacja drgań i kreślenie widm oscylacyjnych;
  • obsługa krystalograficznych komórek elementarnych;
  • generowanie wejścia dla pakietów chemii kwantowej Gaussian, GAMESS i MOLPRO;
  • elastyczna architektura wtyczek i skryptów Pythona.

Avogadro odczytuje formaty plików takie jak: PDB, XYZ, CML, CIF, Molden oraz dane wyjściowe: Gaussian, GAMESS i 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
free molecular modeling and molecular graphics tool
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BALLView provides fast OpenGL-based visualization of molecular structures, molecular mechanics methods (minimization, MD simulation using the AMBER, CHARMM, and MMFF94 force fields), calculation and visualization of electrostatic properties (FDPB) and molecular editing features.

BALLView can be considered a graphical user interface on the basis of BALL (Biochemical Algorithms Library) with a focus on the most common demands of protein chemists and biophysicists in particular. It is developed in the groups of Hans-Peter Lenhof (Saarland University, Saarbruecken, Germany) and Oliver Kohlbacher (University of Tuebingen, Germany). BALL is an application framework in C++ that has been specifically designed for rapid software development in Molecular Modeling and Computational Molecular Biology. It provides an extensive set of data structures as well as classes for Molecular Mechanics, advanced solvation methods, comparison and analysis of protein structures, file import/export, and visualization.

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
Parsery i algorytmy dla chemii obliczeniowej
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Biblioteka Pythona, która zapewnia analizatory składni plików dziennika chemii obliczeniowej. Udostępnia także platformę do implementacji algorytmów w sposób niezależny od pakietu.

Ten pakiet zawiera skrypty pomocnicze dla użytkowników końcowych.

Testy jednostkowe i pliki danych, zarządzane przez cclib, dystrybuowane są oddzielnie np. w niewolnym pakiecie 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.

Please cite: Larry W. Finger, Martin Kroeker and Brian H. Toby: DRAWxtl, an open-source computer program to produce crystal-structure drawings. (eprint) J. Appl. Cryst. 40:188-192 (2007)
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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.

slurm-wlm-torque and gridengine-client are workload managers which provide wrappers for PBS commands. Gabedit also allows one to configure it for any other workload manager.

Please cite: Abdul-Rahman Allouche: Gabedit - A graphical user interface for computational chemistry softwares. (eprint) J. Comp. Chem. 32:174-182 (2011)
gamgi
Ogólny Interfejs Graficzny do Modelowania Atomistycznego
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GAMGI (General Atomistic Modelling Graphic Interface) udostępnia interfejs graficzny do budowania, przeglądania i analizowania struktur atomowych. Program jest skierowany do społeczności naukowej i zawiera interfejs graficzny do badania struktur atomowych i przygotowywania obrazów do prezentacji oraz do nauczania budowy materii atomowej.

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
Analizowanie i wyświetlanie plików wyjściowych Gaussian, GAMESS itd.
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GaussSum analizuje pliki wyjściowe ADF, GAMESS, GAMESS-UK, Gaussian, Jaguar i obliczenia z PC GAMESS, aby zdobyć użyteczne informacje.

GaussSum używa GNUPlot-a do wyświetlenia postępu optymalizacji geometrii, gęstości stanów widma, widma UV-VIS, widma IR, widma Ramana, i map różnic gęstości elektronowej. Może również wyświetlać wszystkie linie zawierające dowolne wyrażenia i nie tylko to.

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
Wizualizator symulacji dynamiki molekularnej
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Jest to program graficzny gpdc, służący do wizualizacji danych wyjściowych pochodzących z symulacji dynamiki molekularnej. Obsługuje on standardowy format xyz, a także inne formaty jako dane wejściowe oraz formaty plików graficznych JPG i PNG jako dane wyjściowe.

jmol
Przeglądarka molekularna
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Jmol to przeglądarka molekularna do trójwymiarowych struktur chemicznych, napisana w języku Java. Jmol umożliwia odczytywanie różnych typów plików i danych wyjściowych z programów chemii kwantowej oraz animację plików wieloklatkowych i obliczonych trybów normalnych z tychże programów. Program udostępnia funkcje do chemikaliów, kryształów, materiałów i biomolekuł. Jmol może być przydatny dla studentów, nauczycieli oraz badaczy chemii i biochemii.

Formaty plików odczytywane przez Jmol obejmują: PDB, XYZ, CIF, CML, MDL Molfile, Gaussian, GAMESS, MOPAC, ABINIT, ACES-II, Dalton i 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
Układ okresowy pierwiastków i narzędzia chemiczne
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Kalzium jest w pełni funkcjonalną aplikacją chemiczną, obejmującą układ okresowy pierwiastków, opis zagadnień z zakresu chemii, rozwiązywanie równań chemicznych oraz podgląd cząsteczek w 3D.

Pakiet jest częścią modułu edukacyjnego KDE.

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VersionURL
22.12.3https://screenshots.debian.net/shrine/screenshot/24823/simage/large-b37a5de92bf3698c7145844e1ea4a4bd.png
21.08.0https://screenshots.debian.net/shrine/screenshot/simage/large-3714f02b9e759819c082b9d19227dccd.png
21.12.3https://screenshots.debian.net/shrine/screenshot/simage/large-7ac385be3f63bd95d07fa6b5ed246c93.png
4:20.04.0-1https://screenshots.debian.net/shrine/screenshot/19284/simage/large-c4639dd58a0b434a43f09b7bd601a95e.png
21.12.3https://screenshots.debian.net/shrine/screenshot/simage/large-b337656907b2f4c884df0e2fef25b617.png
4:4.4.5-1https://screenshots.debian.net/shrine/screenshot/4862/simage/large-e344f66fe538f46bc890f8ed79d12678.png
4:3.5.9-2https://screenshots.debian.net/shrine/screenshot/1228/simage/large-6d015b0dadb288a0cc6f6e5d5d3331fa.png
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qutemol
interactive visualization of macromolecules
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QuteMol is an interactive, high quality molecular visualization system. It exploits the current GPU capabilities through OpenGL shaders to offer an array of innovative visual effects. QuteMol visualization techniques are aimed at improving clarity and an easier understanding of the 3D shape and structure of large molecules or complex proteins.

Qutemol uses advanced OpenGL techniques and might not work correctly with all video cards and drivers.

Features QuteMol offers include:

  • Real time ambient occlusion
  • Depth aware silhouette enhancement
  • Ball-and-stick, space-filling and liquorice visualization modes
  • High resolution antialiased snapshots for creating publication quality renderings
  • Automatic generation of animated gifs of rotating molecules for web page animations
  • Interactive rendering of macromolecules (>100k atoms)

QuteMol reads PDB files as input.

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
Narzędzia do generowania obrazów białek lub innych cząsteczek
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Raster3D to zestaw narzędzi do generowania wysokiej jakości obrazów rastrowych białek lub innych cząsteczek. Główny program renderuje kule, trójkąty, cylindry i powierzchnie kwadratowe z podświetlaniem lustrzanym, cieniowaniem i cieniowaniem Phonga. Stosuje wydajny algorytm programowy Z-buffer, który jest niezależny od karty graficznej. Programy pomocnicze przetwarzają współrzędne atomowe z plików PDB (Protein Data Bank) w celu renderowania opisów obrazów składających się ze wstążek, atomów wypełniających przestrzeń, wiązań, kulki + kija itp. Raster3D może być również używany do renderowania obrazów utworzonych w innych programach, takich jak Molscript, w środowisku 3D z podświetleniami, cieniami itp. Dane wyjściowe zapisywane są w plikach obrazów pikselowych z 24-bitową informacją o kolorze każdego piksela.

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
Graficzny interfejs użytkownika dla SHELXLe
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ShelXle łączy edytor z podświetlaniem składni dla związanych z SHELXL plików wejściowych .ins i plików wyjściowych .res z interaktywnym wyświetlaczem graficznym wyświetlającym trójwymiarowe struktury, w tym mapy gęstości elektronowej (Fo) oraz mapy różnic gęstości (Fo-Fc).

https://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)
v-sim
Wizualizacja struktur atomowych
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V_Sim wizualizuje struktury atomowe, takie jak kryształy, granice ziaren, cząsteczki itd. (w formacie binarnym lub w formacie zwykłego tekstu).

Renderowanie odbywa się w pseudo 3D z kulkami (atomami) lub strzałkami (spinami). Użytkownik może wchodzić w interakcje za pomocą wielu funkcji, aby wybrać widok, ustawić powiązania, narysować płaszczyzny cięcia, obliczyć powierzchnie z pól skalarnych, zduplikować węzły, zmierzyć geometrię itd. Ponadto, V_Sim umożliwia eksportowanie widoku jako obrazu w formatach PNG, JPG, PDF (bitmapa), SVG (schemat) i innych formatach. Dostępne są również narzędzia do kolorowania atomów z wartości danych lub do animowania na ekranie wielu plików pozycji.

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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.

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xbs
3-d models and movies of molecules
Maintainer: Matthew Vernon
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xbs ball-and-sticks plotting program can create still and moving three dimensional models of molecules. X11 and PostScript output are available. Models can be rotated, scaled, etc. Various labeling, shading, lighting, coloring options are available.

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xcrysden
Crystalline and Molecular Structure Visualizer
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XCrySDen is a crystalline and molecular structure visualisation program, which aims at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated. It can run on most UNIX platforms, without any special hardware requirements.

XCrySDen allows for real-time capture of display. Several movie encoders are supported, in particular for Animated-GIF convert (imagemagick), gifsicle, or whirlgif are necessary. For AVI/MPEG mencoder or ppmtompeg (netpbm) is required. For window dumps either imagemagick or xwd (x11-apps) needs to be present.

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xmakemol
Program do wizualizacji układów atomowych i molekularnych
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XMakemol jest programem obsługiwanym za pomocą myszki, napisanym przy użyciu zestawu widżetów LessTif, służącym do przeglądania i zarządzania układami atomów oraz innymi chemicznymi układami. XMakemol wczytuje dane wejściowe XYZ i wyświetla atomy, wiązania i wiązania wodorowe.

Do jego funkcji należą:

  • animowanie plików zawierających wiele klatek;
  • interaktywne mierzenie długości wiązań, kątów pomiędzy nimi oraz kątów skręcenia;
  • kontrolowanie rozmiaru atomu/wiązania;
  • eksportowanie do formatów XPM, Encapsulated PostScript oraz XYZ;
  • przełączanie widzialności poszczególnych grup atomów;
  • edytowanie pozycji podzbiorów atomów.
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