OpenScience / Software / Chemistry



Viewmol

Posted on March 1, 2001 by Dan Gezelter

Viewmol is an open source graphical front end for computational chemistry programs. It is able to graphically aid in the generation of molecular structures for computations and to visualize their results. Find Viewmol at: http://viewmol.sourceforge.net/

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Posted in Molecule Viewers and Editors | Leave a comment

XBS

Posted on March 1, 2001 by Dan Gezelter

XBS is a simple but very useful program for plotting ball-and-sticks models of molecules or crystals under the X Window system. Find XBS at: http://www.ccl.net/chemistry/resources/software/X-WINDOW/xbs/index.shtml

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Posted in Molecule Viewers and Editors | Leave a comment

XMakemol

Posted on March 1, 2001 by Dan Gezelter

XMakemol is a program written for UN*X operating systems in ANSI C using the X, Xt and Motif libraries. It can be used to view and manipulate atomic and molecular data given in xyz format. Find XMakemol at: http://www.nongnu.org/xmakemol/

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ORTEP

Posted on February 28, 2001 by Dan Gezelter

Oak Ridge Thermal Ellipsoid Plot Program for Crystal Structure Illustrations Find ORTEP at: http://www.ornl.gov/ortep/ortep.html

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Posted in Crystallography | Leave a comment

PROCHECK

Posted on February 28, 2001 by Dan Gezelter

Checks the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry. Find PROCHECK at: https://www.ebi.ac.uk/thornton-srv/software/PROCHECK/

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PyMOL

Posted on February 28, 2001 by Dan Gezelter

PyMOL is a molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations. Find PyMOL at: http://pymol.sourceforge.net/

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QMOL

Posted on February 28, 2001 by Dan Gezelter

Qmol is a program for viewing molecular structures and animating molecular trajectories. Find QMOL at: http://www.ccl.net/cca/software/MS-WIN95-NT/qmol/index.shtml

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Raster3D

Posted on February 28, 2001 by Dan Gezelter

Raster3D is a set of tools for generating high quality raster images of proteins or other molecules. Find Raster3D at: http://www.bmsc.washington.edu/raster3d/raster3d.html

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RnaViz

Posted on February 28, 2001 by Dan Gezelter

RnaViz is a user-friendly, portable, GUI program for producing publication-quality secondary structure drawings of RNA molecules. Drawings can be created starting from DCSE alignment files if they incorporate structure information or from mfold ct files. The layout of a structure … Continue reading →

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Posted in Biochemistry | Leave a comment

SCORE

Posted on February 28, 2001 by Dan Gezelter

SCORE is an empirical method developed for estimating the binding affinity of protein-ligand complex with known three-dimensional structure. Find SCORE at: http://mdl.ipc.pku.edu.cn/drug_design/work/score.html

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Posted in Biochemistry | Leave a comment