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Molecular viewers

It has been proved to be useful to provide universal availability of consistent browsers and helper applications via Cabinet servers. The download server is a convenient place for browser, PDB viewer and PDB helper downloads. The combination of Netscape [44] as a browser and PyMOL [45] as a molecular viewer seems to work weU. Other options are available. [Pg.256]

Is a 3 Dimensional molecular viewer which shows molecular models and provides geometry editing capabilities Allylamine... [Pg.161]

Figure 7.12. The structure of 1HMF rendered using Cn3D version 3.0, an interactive molecular viewer that acts as a plug-in to Web Entrez. Cn3D is also bundled with and can be used with Network Entrez. Details are given in the text. Figure 7.12. The structure of 1HMF rendered using Cn3D version 3.0, an interactive molecular viewer that acts as a plug-in to Web Entrez. Cn3D is also bundled with and can be used with Network Entrez. Details are given in the text.
MCDL available at http //mcdl.sourceforge.net/ is another free open-source small Java molecular viewer/editor for chemical stmctures, stored in Modular Chemical Descriptor Language linear notation only [26]. [Pg.10]

Cover images The photograph of raw isinglass was kindly provided by Juanita Navarro the model of a stretch of a collagen molecule is based on 1 cag data in the Protein Data Bank www.pdb.org/ rendered by David Goodsell using the Python Molecular Viewer. [Pg.13]

The 3DB Browser has a number of features that make it easy to access information found in PDB entries. Users can search according to any combination of such fields as compound name, experiment title, authors (depositors), biological source, journal references, date of deposition, and nature of small molecules (heterogens) complexed with the structure. Boolean operators allow highly complex search strings. Entries selected can be retrieved automatically, and the molecular structures can be displayed using the public-domain molecular viewer RasMol, Netscape s Chemscape Chime plug-in. [Pg.2162]

Some of the stand-alone programs mentioned above have an integrated modular 3D visualization application (e.g., ChemWindow —> SymApps, ChemSketch —> ACD/3D Viewer, ChemDraw —> Chem3D). These relatively simple viewers mostly generate the 3D geometries by force-field calculations. The basic visualization and manipulation features are also provided. Therefore, the molecular models can be visualized in various display styles, colors, shades, etc. and are scalable, movable and rotatable on the screen. [Pg.146]

ISlS/Draw has no genuine molecular visualization tool. The rotate tool changes only the 2D rotate tool into a 3D rotate tool which rotates 2D structures in three dimensions. In order to visualize chemical structures in different styles and perspectives, it is necessary to paste the drawing, e.g., to the ACD/3D Viewer. [Pg.146]

Chcm3D is much more than a molecule viewer. This autonomous software module from the ChemOffice package provides simple molecule editor tools to create structures, but is mainly used as a molecular modeling tool. [Pg.147]

Description 3D viewer molecular 3D viewer 2D editor. 3D viewer 3D viewer 3D viewer 3D viewer crystallo- 3D viewer ... [Pg.151]

Molecular dynamics simulation package with various force field implementations, special support for AMBER. Parallel version and Xll trajectory viewer available. http //ganter.chemie.uni-dortmund.de/MOSCITO/... [Pg.400]

Molden can display molecular geometries in a variety of formats, including lines, tubes, ball and stick, ribbons, and CPK. The user has some control over colors and sizes. Molden also has features designed for the display of proteins and crystal structures. The display can be exported as postscript, VRML, Povray, and image files. It can also be configured as a chemical mime viewer. [Pg.350]

WebLab Viewer gives a very-high-quality display suitable for publication and presentation. Molecules can be displayed as lines, sticks, ball and stick, CPK, and polyhedrons. In addition, different atoms within the same structure may be displayed in different ways. Text can be added to the display as well as labeling parts of the structure in a variety of ways. The user has control over colors, radii, and display quality. The program can also replicate a unit cell to display a crystal structure. Several types of molecular surfaces can be displayed. [Pg.352]

Contact information Molecular Simulations, Inc. 9685 Scranton Road San Diego, CA 92121-3752 (888) 249-2292 http //www.msi.com/viewer... [Pg.352]

If a molecule is rotated by changing the position of the viewer (left mouse button rotation) then the molecule s position in the molecular coordinate system has not changed and another contour plot can be requested without recomputing the wave function. That is, many orbitals can be plotted after a single point ab initio or semi-empirical calculation. Any contour map is available without recomputation of the wave function. [Pg.244]

The QCRNA database is viewable and searchable with a web browser on the internet and it is also contained as a MySQL database that is easily incorporated with parameter optimization software to allow for the rapid development of specific reaction parameters. Molecular structures can be viewed with the JMOL [47, 48] or MOLDEN [49, 50] programs as viewers for chemical MIME types. If the web browser is JAVA-enabled, then the JMOL software will automatically load as a web applet. Both programs allow the structure to be manipulated, i.e., rotated, scaled, and translated, and allow for measurement of internal coordinates, e.g., bond lengths, angles, and dihedral angles. Similarly, animations of the vibrational frequencies are available and can be viewed with either program. [Pg.380]

Excitation and emission spectra of molecules for donor-acceptor pairs can be found at one of the following Web sites Becton-Dickinson Fluorescence Spectrum Viewer (http //www. bdbiosciences.com/spectra), Invitrogen-Molecular Probes Fluorescence Spectra Viewer (http //www.probes.invitrogen. com/servlets/spectraviewer). [Pg.176]

The importance of visual inspection Visual inspection of reactants and product molecules offers a library designer tremendous value in terms of what product molecules can or cannot be synthesized to help formulate and address SAR hypotheses. Project medicinal chemists have fondly called this popular approach cerebral processing. PGVL Hub has provided a capable environment to enable this approach (e.g., Structural Viewer panel with many molecules per page for fast browsing, sorting of displayed molecules by molecular properties, and multiple color markers to label molecules for further processing). [Pg.334]

Molecular graphics viewer for PCs and workstations RasMol http //zvzvw.bemstein-plus-sons.com/software/rasmol... [Pg.149]

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See also in sourсe #XX -- [ Pg.265 ]

See also in sourсe #XX -- [ Pg.265 ]



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