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Topic: 3D crystallographic group

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	Crystallography - Wikipedia, the free encyclopedia
		Crystallographic methods now depend on the analysis of the diffraction patterns that emerge from a sample that is targeted by a beam of some type.
		Crystallographers often explicitly state the type of illumination used when referring to a method, as with the terms X-ray diffraction, neutron diffraction and electron diffraction.
		In many cases, an image of a microscopic object is generated by focusing the rays of the visible spectrum using a lens as in light microscopy.
	en.wikipedia.org /wiki/Crystallography (1462 words)

	[cryst] 2 Affine crystallographic groups (Site not responding. Last check: 2007-10-21)
		For instance, if the lower Wyckoff position consists of a space group orbit of lines (and thus the upper one of an orbit of points), the label of the connection line is the number of lines in the orbit which cross a fixed representative point of the upper Wyckoff position.
		in the group of all unimodular transformations of the lattice spanned by the
		Space groups with a centered lattice are therefore given in the non-primitive basis crystallographers are used to.
	www-groups.dcs.st-and.ac.uk /gap/Manuals/pkg/cryst/htm/CHAP002.htm (2609 words)

	Crystallographic Topology - Lattice Complexes
		All other space groups with the same lattice complex are subgroups of that characteristic space group, but not all the subgroups contain the lattice complex (i.e., being a subgroup is a necessary but not sufficient condition).
		3d (#220) produces "I" when the variable x in x,x,x (i.e., on the body diagonal 3-fold axis) is set to zero since in that space group there is no fixed point at 0,0,0.
		Thus the bcc rhombohedral dodecahedron coordination polyhedron (12 faces, 24 edges, 14 vertices) is not dual to the bcc truncated octahedron Dirichlet polyhedron (Loeb,1970), and it serves as a classic counterexample to the postulated duality.
	www.ornl.gov /sci/ortep/topology/lattice.html (2532 words)

	Crystallographic Topology - Cubic Groups
		The 36 cubic crystallographic space groups are different from the remaining 194 space groups in that they each have body diagonal 3-fold axes arising from their tetrahedral and octahedral point groups.
		The seven rhombohedral trigonal subgroups of the cubic groups are shown in the bottom row of the figure with their space group symbols and simplest lattice complex in the top row of each box.
		Crystallographic color groups and the concept of antisymmetry are discussed in Appendix A. In the bicolor space groups, there are 1191 out of the total of 1651 group members that have mixed symmetry and antisymmetry group elements.
	www.ornl.gov /sci/ortep/topology/cubicgsg.html (1827 words)

	Getting Started with the CSD - 1.3 Links Between Chemistry and Crystallography in the CSD (Site not responding. Last check: 2007-10-21)
		A crystal structure consists of a basic atomic motif that is repeated in 3D space according to the symmetry operators of the crystallographic space group.
		The crystallographer determines the 3D coordinates of the atoms in this basic motif or asymmetric unit and the extended crystal structure then follows by application of the space group symmetry.
		This means that the crystallographic asymmetric unit contains one half of the p-dinitrobenzene molecule and one half of the tetrathiafulvalene molecule.
	www.sdsc.edu /CCMS/Packages/cambridge/started/gs-1-3.html (504 words)

	The Geometry Junkyard: Symmetry and Group Theory
		The MSRI Computing Group uses another horoball diagram as their logo.
		Jonathan A. Poritz and coworkers investigate the fundamental domains of cyclic group actions on hyperbolic 3-space, resulting in lots of pretty pictures of overlapping spheres.
		Group theoretic mathematics for determining whether a polygon formed out of hexagons can be dissected into three-hexagon triangles, or whether a polygon formed out of squares can be dissected into restricted-orientation triominoes.
	www.ics.uci.edu /~eppstein/junkyard/sym.html (1155 words)

	Coherent Imaging Group at UCLA
		“3D Coherent Diffraction Microscopy and Its Applications in Nanoscience and Structural Biology”, Symposium on Synchrotron Radiation for the International Chemical Congress of Pacific Basin Societies, Honolulu, Hawaii, Dec. 15-20, 2005.
		“3D Coherent X-ray Diffraction Microscopy: the Present and the Future”, PSI Workshop on Pixel- and Microstrip-Detectors for Synchrotron Radiation, Paul Scherrer Institut, Switzerland, Oct. 18-19, 2005.
		“3D Diffraction Microscopy and Its Applications in Structural Biology”, the 8th International Conference on Biology and Synchrotron Radiation, Himeji, Japan, Sep. 7-11, 2004.
	www.physics.ucla.edu /research/imaging/talks (841 words)

	3D searching with Receptor-based queries
		A major application for 3D databases is pharmacophoric searching, which finds molecules that have essential functional groups in the proper position to interact with a given receptor.
		The terminal phenethyl group in enalapril presumably interacts with a lipophilic region of the ACE receptor, which was a part of the conceptual model of the enzyme developed earlier (site S1).
		Therefore, we developed a 3D querying strategy that utilizes the available information from receptor-sites with bound ligands, as well as information that can be gathered from the patterns recognized from a list of known active compounds.
	www.ch.ic.ac.uk /ectoc/papers/guner (4105 words)

	Department of Molecular Biosciences (Site not responding. Last check: 2007-10-21)
		In biological systems, there are a myriad of reactions in which methyl groups are transferred from a few types of methyl donor molecules to a wide variety of methyl acceptor molecules.
		The 3D structures of several enzymes that are involved in the methyl cycle have been determined.
		On the basis of the 3D structures, the catalytic mechanisms of the enzymes have been proposed.
	molecularbiosciences.ku.edu /bcmpcb/takusag.html (353 words)

	Physical Biosciences Division at Berkeley Lab (Site not responding. Last check: 2007-10-21)
		The key to understanding the inner workings of cells is to learn the three-dimensional atomic structures of the full repertoire of macromolecules that form their architecture and carry out their metabolism.
		These three-dimensional (3D) structures are encoded in the blueprint of the DNA genome.
		Within the Computational Structural Biology group in the Physical Biosciences Division's there are individual research programs in the areas of protein structure prediction and folding, RNA structure prediction and classification and RNA gene discovery, and computational tools for macromolecular structure determination and analysis by x-ray and cryo-EM.
	www.lbl.gov /pbd/ctb (691 words)

	ICM User's Guide: Working with the PDB
		P2121 that determine N (depends on a group) transformations for the atoms in the asymetric unit.
		To generate the coordinates within one cell one needs to apply N transformations and then to generate neigboring cells the content of one cell needs to be translated in space according to the cell position.
		The crystallographic symmetry neighbors will be displayed in the Workspace Panel along with the crystallographic cell.
	www.molsoft.com /gui/pdb.html (1716 words)

	PreQuest: 3D Check
		Crystallographic Properties relates to the set of operations which can be performed on the structure based on the inherent geometrical and spacial information available.
		It is vital that every molecule in the 3D structure matches a molecule in the 2D diagram because the Quest search for 3D geometric structures will not access the 3D co-ordinates unless the match status is "perfect match".
		The 3D structure is displayed with bond types depicted as single, double, and triple lines.
	www.sdsc.edu /CCMS/Packages/Cambridge/prequest/zprq2130.html (1416 words)

	Advanced VRML Based Chemistry Applications: A 3D Molecular Hyperglossary
		This approach was first demonstrated in a series of influential papers in the early 1980s by Taylor, Kennard and Versichel[3], in their discussions of the geometry of the N-H...O=C hydrogen bond.
		It is important to note, however, that the scatterplot is derived from the raw crystallographic data rather than these parameters as additional information is required in the subsequent analysis.
		This 3D distribution function was visualised using custom modules developed as part of our Explorer EyeChem[5] module suite and superimposed upon the crystal cluster diagram.
	www.ch.ic.ac.uk /rzepa/eccc2 (2646 words)

	Modern Instrumental Biochemistry
		These new instrumentation intensive techniques have made possible the growing array of sophisticated projects such as the Human Genome Project (made possible by rugged, high performance capillary electrophoretic chromatography) and the vast number and improved quality of protein 3D structures now available (made possible by improved crystallographic and NMR methods).
		The core development that is driving "Proteomics" is improvements in the sensitivity, automation, resolution, sample handling protocols, and mass accuracy of the mass spectrometers.
		The goal of our research group is to develop and improve the needed mass spectrometry instrumentation with an eye toward applications of biological and medical interest.
	www.bumc.bu.edu /Dept/Content.aspx?DepartmentID=385&PageID=7195 (222 words)

	Lessons from XtalView - CCP4 3d browser. (Site not responding. Last check: 2007-10-21)
		Most 3d applications store a bricked-map on disk, with 'bricks' of contiguous density held in a contiguous block of disk.
		This is less efficient with a simple 3d array than with a bricked map, since whole sections will be held rather than those protions of the section which are being viewed.
		The coding is also more complex than for a simple 3d array, and non-sequantial accesses such as simple fft's will be inefficient (however a resectioning fft will be possible).
	www.ysbl.york.ac.uk /~cowtan/ccp4/3dinfo.html (1322 words)

	ETH Zurich: Research Groups
		The group's research focuses is on the X-ray crystallographic structures of the nucleosome core particle and the chromatosome, two sub-elements of the nucleosome, as well as crystal structures of several transcription factor protein/DNA complexes.
		To explore the range of motion of motor proteins in complex with their partners, structures of each individual (not averaged) particles (a molecule or a complex of molecules) must be visualized at sufficiently high resolution.
		We develop the methodology that fulfills these demands, combining two methods of 3D cryo-electron microscopy: single particle analysis and electron tomography, in order to visualize the structure of motor proteins and their complexes during dynamic motions under the condition close to in vivo.
	www.mol.biol.ethz.ch /groups (932 words)

	Genomics and Proteomics - Making an Enzyme Structure Crystal Clear (Site not responding. Last check: 2007-10-21)
		The structure was solved by crystallographic techniques, revealing a toroidal shape and a novel protein motif.
		Twelve years ago, when Mondragón's group was working on determining the structure of the first eukaroytic yeast type IA topoisomerase sequence, they noticed there was significant similarity between the two type IA enzymes from E.
		If Mondragón's group identifies a protein domain of which they want to study the structure, they first must make several milligrams of the protein.
	www.genpromag.com /ShowPR.aspx?PUBCODE=018&ACCT=1800000100&ISSUE=0307&RELTYPE=PR&ORIGRELTYPE=CVS&PRODCODE=00000000&PRODLETT=E (2750 words)

	Introduction to Quasicrystals
		In contrast to the 3D method this is a quantitative analysis, which allows to calculate diffraction patterns and to refine a variety of parameters by the least-squares method.
		All atom positions in 3D are then obtained from the intersection of the occupation domains with the 3D external space.
		The 230 symmetry groups with rotational and translational symmetry elements, by which normal 3D-structures are characterized.
	www.jcrystal.com /steffenweber/qc.html (3665 words)

	IU Biology Faculty: Tuli Mukhopadhyay
		Right: Cross section of Sindbis virus at 11 Å resolution with the glycoproteins (E1 and E2), the lipid bilayer, and the capsid protein (NCP) all identified (Zhang, Mukhopadhyay et al., 2002).
		Budding of alphavirus particles is an ordered process requiring that the C-terminus of the integral membrane E2 glycoprotein first bind to a "pocket" of the capsid protein in cytoplasmic nucleocapsid cores.
		In order to understand the molecular mechanisms at the different stages of the virus life cycle, my group will employ structure-function studies using a combinatorial approach of genetics, biochemistry and structure determination.
	www.bio.indiana.edu /facultyresearch/faculty/Mukhopadhyay.html (583 words)

	Macromolecural Structures Group - Projects
		The work on the former two types is mainly crystallographic, while the zinc-fingers interactions are being approached via a statistical analysis of their sequences and their relation to their DNA targets.
		Depending on which atom the methyl group is transferred to, methylases are classified as m5C-methylases (transfer to the C5 atom of cytosine bases), m4C- (to the N4 atom of cytosines) and m6A-methylases (transfer to the N6 atom of adenines).
		The enzyme has been crystallized using PEG 6000 in space group P21 with a=53.7, b=85.7, c=151.8 (Angstroem) and â=95.1o and two molecules in the asymmetric unit.
	www.imbb.forth.gr /groups/macromolec/projects/2.html (526 words)

	51M05: General Euclidean geometry
		The actions of the point groups among the crystallographic groups are the basis for the construction of the Platonic solids and the regular divisions of the sphere in R^3.
		Suppose L is a set in space such that all lines through 2 points in L passes through a third.
		Subdivisions of the sphere corresponding to the actions of the dihedral group.
	www.math.niu.edu /~rusin/known-math/index/51M05.html (329 words)

	Crystallographic group - Wikipedia, the free encyclopedia
		A crystallographic group is a topologically discrete subgroup of the group of isometries of some geometric space (typically, not necessarily a Euclidean space) with a compact fundamental domain.
		For 3D Euclidean space, see space group and crystallographic point group.
		This page was last modified 10:53, 5 July 2006.
	en.wikipedia.org /wiki/Crystallographic_group (71 words)

	Synthesis and Solid-State Self-Assembly of Polyphenols (Site not responding. Last check: 2007-10-21)
		A simple synthetic strategy for polyphenols (1-3) is outlined, and their crystallographic investigations are described.
		Interesting self-assembled structures were observed in the crystal lattice owing to the 3D structure and hydrogen-bonding interactions between the hydroxyl groups.
		In all the above structures, both the number and the position of the hydroxyl groups on the triphenylmethane core play an important role in the formation of supramolecular architectures.
	pubs.acs.org /cgi-bin/abstract.cgi/cgdefu/2004/4/i03/abs/cg0341508.html (199 words)

	MMDB Help
		NCBI has developed a 3D structure viewer, Cn3D, for easy interactive visualization of molecular structures from Entrez.
		MMDB structural data of proteins are compared against each other using the VAST algorithm for detecting significantly similar substructures.
		The detection of structural similarity in the absence of obvious sequence similarity is a powerful tool to study remote homologies and protein evolution.
	www.ncbi.nlm.nih.gov /Structure/MMDB/mmdbhelp.html (152 words)

	Dr Garrett M. Morris
		CCDC: Cambridge Crystallographic Data Centre and the Cambridge Structural Database, CSD, of organic and metal organic compounds.
		There is a good discussion of the generation and use of large 3D databases in drug discovery which is accessible on-line, from the September 1995 issue of NetSci.
		VMD - Visual Molecular Dynamics from the Theoretical Biophysics Group at the University of Illinois at Urbana-Champaign.
	www.scripps.edu /mb/olson/people/gmm/index.html (3985 words)

	Comparing Chemical Databases
		3D biological macromolecular structure data, primarily determined by X-ray crystallography and NMR
		Includes atomic coordinates, space group symmetry, covalent radii and crystallographic connectivity.
		Includes 3D molecular structure and crystal structure models.
	www.dartmouth.edu /~krescook/instruct/chemtable.shtml (302 words)

	Dictionary Resources
		The PDB Exchange data dictionary consolidates content from a variety of crystallographic dictionaries including: the IUCr Core, mmCIF, Image and symmetry dictionaries.
		Community extension data dictionary describing 3D EM structure and experimental data to be deposited in the EMDB and PDB databases.
		Development version of the 3D EM data dictionary for program to program data exchange.
	mmcif.pdb.org /index.html (272 words)

	[No title] (Site not responding. Last check: 2007-10-21)
		EXAFS (Extended X-ray absorption fine structure) refers to the sinusoidal variation of the X-ray absorption coefficient as a function of X-ray photon energy, which occurs after each absorption edge of an element and extends for up to 1500 eV further.
		The Service Crystallography Special Interest Group was formed to provide a forum for professional service crystallographers.
		The Small Molecule Special Interest Group was formed to promote all aspects of the application of crystallographic techniques to the determination, analysis and presentation of structures of small molecules.
	www.anachem.umu.se /jumpstation/X-RaySpectroscopy.html (259 words)

	Structural Biology
		It's main focus is the three-dimensional structure determination of macromolecules using crystallographic diffraction or nuclear magnetic resonance (NMR) data.
		Bibliographic, 2D chemical and 3D structural results from crystallographic analyses of organics, organometallics and metal complexes.
		It is developed by the Theoretical Biophysics Group at the Beckman Center, University of Illinois.
	helix.nih.gov /science/structbio (672 words)

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