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Topic: Molecule editor

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	Researchers demonstrate single molecule absorption spectroscopy
		Unlike single molecule fluorescence spectroscopy, which is now a commonly used measurement technique, single molecule absorption spectroscopy has been an elusive goal.
		"First, the sample molecule is placed on a transparent silicon substrate," said Joseph Lyding, a professor of electrical and computer engineering and a researcher at the Beckman Institute.
		"Single molecule absorption spectroscopy is an extremely sensitive technique for analytical chemistry, for measuring electrical properties of molecules, and for studying energy transfer on surfaces," Gruebele said.
	www.eurekalert.org /pub_releases/2005-12/uoia-rds122005.php (453 words)

	Molecule editor - Wikipedia, the free encyclopedia
		A molecule editor is a computer program for drawing and editing chemical structures.
		There also exist three-dimensional molecule editors for the construction of molecule models, usually as part of molecular modelling software packages.
		Files generated by two- or three-dimensional molecule editors can also be displayed by a molecule viewer, which can be realized as a small applet to show molecules in web pages.
	en.wikipedia.org /wiki/Molecule_editor (158 words)

	[No title]
		Its team of PhD-trained scientific editors works closely with authors, reviewers, and the scientific editorial board to ensure that the high standards of the journal are maintained while publishing breaking discoveries and the best in molecular mechanisms.
		In the limited number of instances where a paper is potentially appropriate in scope for the readership of two different Cell Press titles, the Cell Press journals also offer authors a unique opportunity not provided by any other journal group to submit a manuscript for joint consideration at two journals at the same time.
		The editors reserve the right to seek comments from reviewers or additional information from authors on any cases in which concerns arise.
	www.molecule.org /misc/authors.shtml (4869 words)

	Chemistry 347
		The purpose of Mechanics is to investigate conformational energy of a molecule.
		The theoretical basis of MOPAC is to calculate the molecular orbitals (MO's) of the molecule, from which energy and electron density may be calculated.
		Many of the commands in Visualizer+ are similar to commands in Editor; however, it is possible only to look at molecules and not to change molecular geometry or energy in the molecule file.
	www.chem.hope.edu /~polik/Chem347-1999/ComputationalChemistry.htm (1271 words)

	Chapter 14 -- Molecule Components and Construction
		The Molecule Editor is the tool for editing the existing database molecules and for creating new basic molecules from scratch.
		Note Although you can add molecule fragments directly from the Construct/Design dialog box, it is much more convenient to add them in advance (before calling up the dialog) with the help of the Fragment Wizard—the tool specifically designed for visual selection of molecule fragments from Molecule Display windows.
		If the new molecule is unsequenced, it’s easier to construct it first from one DUMMY fragment using Construct/Design Molecule dialog box, and then enter its functional and restriction maps loading the molecule from the database into the Molecule Editor.
	pastime.cgu.edu.tw /petang/Bioinfomatics/MANUALS/VectorNTI/14_(Molecule_Components_and_Construction).html (6026 words)

	7.2 Adding or replacing atoms
		While building a molecule bond lengths of newly created bonds are set to 90 % of the sum of the atomic radii of the bonded atoms and bond angles are assigned according to the coordination.
		The torsion angle is always measured along the backbone of a molecule, i.
		The backbone of a molecule is determined by counting all atoms attached to one atom and following the bonds which connect the atoms with the largest number of other atoms attached.
	viewmol.sourceforge.net /documentation/node14.html (557 words)

	Ertl, Jacob / WWW-based Chemical Information System
		The system enables easy retrieval of molecules from the corporate database, generation and editing of structures using a novel molecular editor written in Java, on-line calculation of hydrophobic and electronic physicochemical properties, generation of molecular images of various types and simple QSAR analysis.
		Hydrophobic properties express the ability of a molecule to be transported in the environment and in an organism, to interact with biological membranes, and to be bound to a receptor by hydrophobic forces.
		Similarity of two molecules is calculated simply as a distance between two points in the n-dimensional space of (properly scaled) molecular properties.
	www.elsevier.com /homepage/saa/eccc3/paper6 (1470 words)

	Chapter 15 -- Database Operations (Site not responding. Last check: )
		Molecules that have as a direct ancestor any one of the molecules shown in this dialog will be found by the search.
		If more than one molecule is selected, the Explorer allows you to choose between FASTA format and Vector NTI Archive format for transferring the selected molecules to the file system target (either via copy/paste or drag/drop).
		Since molecule is most commonly used kind of Vector NTI database object, Vector NTI allows you to view and edit User Fields in the Text panes of Molecule Display windows.
	www.biology.lsa.umich.edu /research/vnti/Documentation/vectornti/15_(Database_Operations).html (13976 words)

	Morphing Methods
		Examples of XYZ animations are an alpha helix in thermal motion and vibrations corresponding to peaks in an IR spectrum.
		If you are particularly interested in the conformational changes of a small portion of the molecule, such as an active site, it may be preferable to align just that portion, rather than the entire molecule.
		If there are conformational changes in distant parts of the molecule, whole-molecule alignment may cause the portion of interest to translate or rotate an a manner unrelated to conformational changes within that portion.
	www.umass.edu /microbio/chime/morpher/morphmtd.htm (3551 words)

	OpenTeach Group - e-Learning Technologies & Software Development (Site not responding. Last check: )
		Chem2D/3D Molecule Visualizer is designed for displaying 2D structure formulas and 3D models of molecules.
		The library allows to display a molecule in the form of a 2D structure that can be used in Chemistry textbooks and in the form of a 3D model that can be viewed with a special 3D Visualizer.
		Molecule Visualizer is integrated into a CourseML 2.5 content management platform which allows to insert 2D structural formulas directly into the text of a tutorial.
	www.openteach.com /technologies/chemml.php (192 words)

	WebMO Editor Help
		The WebMO editor is a Java applet that facilitates the entry of the structure of interest in a three dimensional environment.
		This menu item translates the molecule to the center of the editor window, and set the origin of rotation to the center of the molecule.
		Scan information is specified at the bottom of the editor using the start and stop values, as well as the desired number of steps.
	www.webmo.net /~webmodemo/webmo/help/editor_help.html (1431 words)

	Chemists synthesize molecule that helps body battle cancers, malaria
		The first synthesis of QS-21A, a medicinally important molecule that helps the body battle disease, has been achieved by chemists at the University of Illinois at Urbana-Champaign.
		"Now that we have synthesized this remarkable molecule and confirmed its structure, we are in a position to examine how it works and investigate ways to improve its performance," said David Y. Gin, a professor of chemistry at Illinois.
		The molecule could therefore save patients money on expensive drugs and stretch limited supplies of antigens and vaccines.
	www.medicalnewstoday.com /medicalnews.php?newsid=20540 (439 words)

	domain-B : Indian business : infotech : UNESCO's Freeduc comes to India
		Rahul Chopra, editor, 'Linux for You,' expressing his views on the software says, "Freeduc is an interesting proposition for the education fraternity seeking cost-effective and interactive educational solutions.
		The other prominent applications that form part of this section are simulator for classic mechanics, a unit conversion utility, a tool to create maps of the sky, a 3D viewer for molecules, a planetarium, an editor for scientific and structured documents, a sophisticated clock, a periodic table of the elements, and a molecule editor.
		An editor for printed circuit boards, a simulator/ editor for numerical circuits, a morphing utility, a tool for technical drawing, a basic draw utility, an image manipulation and paint program, and an advanced tool for vectorised drawing are also available.
	www.domain-b.com /infotech/itnews/200401jan/20040107_freeduc.html (609 words)

	JME Molecular Editor Applet
		JME Molecular Editor is a Java applet which allows to draw / edit molecules and reactions (including generation of substructure queries) and to depict molecules directly within an HTML page.
		Tha calculation of molecule properties available from the Molinspiration site is not done by JME, but by the Molinspiration property calculation engine, running on the server.
		JME just generates molecule SMILES representation, which is sent for processing to the server.
	www.molinspiration.com /jme/index.html (301 words)

	Sequin help documentation
		This descriptor indicates the characteristics of the molecule from which the sequence was derived.
		In most cases, the molecule and class are the only choices which should be edited from the default values.
		However, if you have sequenced a transgenic molecule, for example, one that is part plant and part bacterial, you would use Biological Source Features to annotate which sequence was derived from plant and which from bacteria.
	www.ncbi.nlm.nih.gov /Sequin/sequin.hlp.html (16107 words)

	ICM User's Guide: Molecular Editor
		To draw a new chemical structure the ICM Molecular Editor should be loaded.
		The undo and redo options for the ICM Molecular Editor are located in the Edit menu and on the toolbar as shown below.
		Molecules drawn in ICM can be cut and pasted into ISIS-Draw and vice-versa molecules from ISIS-Draw can be cut and pasted into ICM.
	www.molsoft.com /gui/molecule-editor.html (1274 words)

	7.3 Example: Building cyclohexane (Site not responding. Last check: )
		The molecule should now look like the left one in the Figure.
		The molecule should now look like the one in the middle of the Figure.
		The molecule will now look like the right one in the Figure.
	viewmol.sourceforge.net /documentation/node15.html (373 words)

	xLEaP (Site not responding. Last check: )
		In addition to the command-line interface contained in the Universe Editor window, it has a Unit Editor (graphical molecule editor), an Atom Properties Editor, and a Parmset Editor.
		This allows users to draw molecules piecemeal and make adjustments as they draw, without worrying that the builder is going to undo their work.
		Another always-available operation when the pointer is in the viewing window is the keyboard spacebar, which centers the view of the molecule, and is especially useful if the UNIT becomes "lost" due to some operation.
	www.unc.edu /atn/asg/applications/amber/amber/doc/html/AMBER-sh-5.7.html (4059 words)

	NCI Database Help
		As an example, we choose Taxol as the drug molecule for which we want to find similar compounds in the NCI database that may have potential drug activity, and want to learn more about them if literature is available.
		We want to limit ourselves to molecules that have not yet been tested in the NCI anti-HIV screen, are of drug-like size, and avoid certain very common classes of compounds against this target.
		If your favorite desktop molecule editor supports CopyandPaste of SMILES strings, you can simply use this editor, put the structure on the clipboard as a SMILES string and paste it into the entry field.
	cactvs.cit.nih.gov /ncidb2/help.html (10959 words)

	CAChe Tutorial
		Most important is that the molecule you created in the Editor actually changes to the structure that corresponds to the energy minimum.
		When you open the molecule file in the Editor and examine it after optimization, the geometry is different, and "better" than the structure you originally created.
		The optimum geometry of the molecule is determined based on changes to the remainder of the molecule.
	www.chem.ox.ac.uk /course/cache/mechanics.html (967 words)

	Index (Marvin API documentation (c) 1998-2005 ChemAxon Ltd.)
		Adds the S-groups of a child molecule clone to the new parent molecule clone.
		Calculates the number of all aliphatic bonds in the molecule excluding bonds connected to hydrogens.
		Calculates the weight of the MS molecule ion using the mass of the most frequent natural isotope for element atoms.
	www.bindingdb.org /bind/chemsearch/marvin/doc/api/index-all.html (1986 words)

	Molecular Modelling Software
		Molecular mechanics and dynamics technique to evaluate the energies and geometries of molecules in vacuo or in solution, and to display and examine graphically the results of the modeling calculations.
		A suite of molecule builders that enable the construction of small molecule, carbohydrate, protein, DNA and crystal structures.
		Molecules are easily constructed with your mouse and pull-down menus.
	www.chemistry-software.com /software_guide/modelling_index.htm (806 words)

	Informax Inc. - Solutions
		Upon being opened by the Viewer, a molecule is loaded in a Molecule Display window.
		If a molecule was opened from a Vector NTI Molecule Document, additional data generated in the full Vector NTI package will be shown but may not be modified or re-created in the Vector NTI Viewer.
		This includes results of a motif search, PCR primers, sequencing primers and hybridization probes, description of the component fragments which were used to construct a molecule, and a "Construction plan" which is the result of Vector NTI molecule design process.
	register.informaxinc.com /solutions/vectornti/molecular_viewer.html (483 words)

	Kalzium 3D Molecule Editor: The Start of My GSoC Project - Marcus D. Hanwell's Blog
		I will be working on the 3D molecular editor project which was an idea proposed by Carten Niehaus on the KDE GSoC 2007 ideas page.
		I was hoping to be able to find an area I could help out with that when I discovered the idea that looked like it had been written for me! I then discovered the Avogadro project and met some of the project's developers.
		Open Babel and the Avogadro library underpin much of the 3D molecular editor and I have already made quite a few commits to the Avogadro and Kalzium subversion repositories.
	blog.cryos.net /archives/141-Kalzium-3D-Molecule-Editor-The-Start-of-My-GSoC-Project.html (1127 words)

	toolkit_notes.html
		Streams of atoms or bonds can be derived from a molecule, streams of datatrees can be derived from a database, streams of molecules can be derived from a reaction.
		When a molecule is deallocated, all atoms and bonds beloning to the parent molecule, and any streams over the molecule, are deallocated.
		SMILES is a language for representing a molecule as an ASCII string.
	www.daylight.com /meetings/summerschool00/course/toolkit (1856 words)

	conned (Site not responding. Last check: )
		The Connection Editor can be used to determine whether proper atom ordering is maintained throughout a molecule group.
		The Connection Editor is used to verify and assign atom equivalencies in two molecular structures.
		When the Connection Editor is active, the molecule will be analyzed to determine if the atom tags match across the entire molecule group, and the status bar will report the result.
	www.gaussian.com /g_gv/conned.htm (372 words)

	WebMO Support Forum
		However, when I click the "Open Editor" button, the Editor opens but I can't draw a molecule.
		Immediately upon opening the editor, RESIZE the window by dragging the lower right hand corner.
		It may be necessary to repeat this each time you enter the Build Molecule page.
	www.webmo.net /discus/support/messages/3/50.html?1018990486 (236 words)

	CLiDE Molecule Editor
		The right mouse button is not used in the Molecule Editor at the moment.
		Selecting this option will cause the "Save molecule" File Selection Window to pop up, allowing the user to specify the format and name of the file to save.
		To do so, select a file using the "Include molecule" File Selection Window (automatically displayed when "Include File" option is selected), then click with the left mouse button on a suitable location to include the molecule.
	www.chem.leeds.ac.uk /ICAMS/CLiDE/help/mol_ed_ui.html (921 words)

	QUANTA: Generating and Displaying Molecules - Editing 3D Structures
		Although the Molecular Editor allows 3D structures to be built by merging a number of molecular fragments, it is often faster and easier to sketch the base structure in ChemNote.
		Restores the structure as it was on entering the molecular editor.
		Although you can build molecules from scratch, it is generally easier to begin construction in ChemNote, moving to the Molecular Editor when you have completed the basic structure.
	www.scripps.edu /rc/softwaredocs/msi/quanta98/gen_display/02_editing_3D.html (5422 words)

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