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
분자 그래픽 및 모델링 시스템
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Avogadro는 분자 및 생체분자를 대상으로 하는 분자 그래픽 및 모델링 시스템입 니다. 분자 궤도 및 정전기 전위와 같은 특성을 시각화할 수 있으며 직관적인 분 자 빌더를 특징으로 합니다.

특징은 아래와 같습니다:

  • 자동 force-field 기반에 지오메트리 최적화 기능을 갖춘 분자 모델러
  • 제약 조건 및 이형태체 검색을 포함하는 분자 역학
  • 분자 궤도 및 일반 등밀도면 시각화
  • 진동의 시각화 및 진동 스펙트럼 플로팅
  • 결정학상의 단위 세포 지원
  • Gaussian, GAMESS 및 MOLPRO 양자 화학 패키지를 위한 입력 생성
  • 유연한 플러그인 아키텍쳐 및 파이썬 스크립팅

Avogadro가 읽을 수 있는 파일 형식은 PDB, XYZ, CML, CIF, Molden 및 Gaussian, GAMESS, MOLPRO 출력입니다.

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
자유 분자 모델링 및 분자 그래픽 도구
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BALLView는 분자 구조, 분자 역학 방법 (최소화, AMBER, CHARMM, 및 MMF94 힘의 장을 사용하는 MD 시뮬레이션), 정전 속성 (FDPB) 및 분자 편집 기능의 계산 및 시각화에 대한 빠른 OpenGL 기반의 시각화를 제공합니다.

BALLView는 특히 단백질 화학자와 생물 물리학자의 가장 일반적인 요구 사항에 초점을 맞춘 BALL (Biochemical Algorithms Library)에 기반한 그래픽 사용자 인 터페이스로 간주될 수 있습니다. Hans-Peter Lenhof (Saarland University, Saarbruecken, Germany)와 Oliver Kohlbacher (University of Tuebingen, Germany) 그룹에서 개발되었습니다. BALL은 분자 모델링및 전산 분자 생물학의 신속한 소프트웨어 개발을 위해 특별히 지속적으로 설계된 C++의 어플리케이션 프레임워크입니다. 분자 역학, 향상된 용매 화법, 단백질 구조의 비교 및 분석, 파일 import/export, 시각화를 위한 광범위한 데이타 구조와 클래스를 제공합니다.

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
크리스탈 구조 뷰어
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DRAWxtl은 단위 셀 파라미터, 공간 그룹, 원자 좌표, 온도 매개 변수 또는 푸리 에 맵을 포함하는 크리스탈 구조의 기본적인 설명을 읽고, 다면체, 평면, 고립 전자쌍 콘, 구 또는 타원체, 결합, iso-surface 푸리에 윤곽, 및 단위 셀 경계를 포함하는 기하학적 객체를 출력합니다.

네개의 그래픽 형식을 만듭니다:

  • 바로 볼 수 있는 OpenGL 윈도우
  • 출판물 품질의 그림을 위한 비전 레이 추적기의 지속성 (Persistence of Vision Ray Tracer/POV-RAY) 장면 언어
  • 인터넷을 통해 제공되는 가상 현실 모델링 언어 (Virtual Reality Modeling Language/VRML)
  • 고품질 출력을 원하지만 POV-RAY는 설치되지 않은 사람들을 위한 OpenGL 윈도우의 포스트스크립트 랜더링.

파일 형식 DRAWxtl은 CIF, FDAT, FullProf (pcr), GSAS, SCHAKAL, SHELX, DISCUS, WIEN2k들을 읽을 수 있습니다.

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Gabedit
Ab Initio 패키지에 대한 그래픽 사용자 인터페이스
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Gabedit는 아래의 계산 화익 패키지에 대한 그래픽 사용자 인터페이스입니다:

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

Ab Initio 소프트웨어 패키지는 내부 또는 외부 서버 (FTP, RSH, SSH를 지원)에 서 실행됩니다. Gabedit는 대부분의 주요 분자 파일 형식을 포함하는 다양한 계 산 결과를 표시할 수 있습니다. 발전되 "분자 빌더"는 분자에서 빠른 스케치와 3D로 그것들을 실험할 수 있도록 합니다. 그래픽은 애니메이션을 포함한 다양한 형식으로 익스포트될 수 있습니다.

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)
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General Atomistic Modelling Graphic Interface (GAMGI)는 원자 구조를 빌드하 고, 보고, 분석하기 위한 그래픽 인터페이스를 제공합니다. 이 프로그램은 과학 커뮤니티를 목적으로 하며, 원자 구조를 연구하고 프리젠테이션을 위해 이미지를 준비하고 물질의 원자 구조를 가르치는 그래픽 인터페이스를 제공합니다.

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
Gaussian, GAMESS 및 기타 출력을 파싱하고 출력
Maintainer: Debichem Team
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GaussSum은 ADF, GAMESS, GAMESS-UK, Gaussian, Jaguar 및 PC HAMESS 계산의 출 력 파일에서 유용한 정보를 추출하기 위해 파싱합니다.

GaussSum은 기하학 최적화, 상태 밀도, UV-VIS 스펙트럼, IR 스펙트럼, 라만 스 펙트럼, 및 선형 밀도 차이등 맵의 진행 상황을 표시하기 위해 GNUPlot을 사용합 니다. 또한 임의 문장을 포함하는 모든 라인을 표시하고 그 이상을 표시합니다.

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
visualiser of molecular dynamic simulations
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gpdc is a graphical program for visualising output data from molecular dynamics simulations. It reads input in the standard xyz format, as well as other custom formats, and can output pictures of each frame in JPG or PNG format.

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Jmol
분자 뷰어
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Jmol은 3차원 화학 구조를 위한 Java 분자 뷰어입니다. 특징으로 다양한 파일 타 입을 읽어 양자 화학 프로그램에서 출력하고, 멀티 프레임 파일 및 양자 프로그 램에서 계산된 일반 모드의 애니메이션을 포함합니다. 화학 물질, 결정체, 자료, 생체 분자에 대한 기능을 포함합니다. Jmol은 화학 및 생화학 분야에 학생, 교육 자 및 연구원에게 유용할 수 있습니다.

Jmol이 읽는 파일 형식으로는 PDB, XYZ, CIF, CML, MDL Molfile, Gaussian, GAMESS, MOPAC, ABINIT, ACES-II, Dalton 및 VASP가 있습니다.

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)
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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
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
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
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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.

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Xbs
분자 3-d 모델 및 영화
Maintainer: Matthew Vernon
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xbs ball-and-sticks 플로팅 프로그램은 정지 및 움직이는 분자 3차원 모델을 만 들수 있습니다. X11 및 포스트스크립트 출력이 가능합니다. 모델은 회전, 확대, 축소등이 가능합니다. 각종 라벨, 음영, 조명, 색상 옵션이 가능합니다.

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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 for visualizing atomic and molecular systems
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Svn

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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