Benutzer:Roo1812/Baustelle
http://www.ingmar-landeck.de/index-llp.html?/deutsch/frames/main/leichhardt/petasida.html Tiere Leichhardt
http://www.thedailylink.com/australiantarantulas/species/index.html Vogelspinnen in Australien :-)
http://australianmuseum.net.au/Australian-tarantulas
http://www.qm.qld.gov.au/Find+out+about/Animals+of+Queensland/Spiders/Primitive+Spiders+Infraorder+Mygalomorphae/Tarantula+or+Whistling+Spiders
Chimera
[Bearbeiten | Quelltext bearbeiten]| UCSF Chimera
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| Datei:Chimera1.png Chimera Hauptfenster ( ... ) | |
| Basisdaten
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| Entwickler | Resource for Biocomputing, Visualization, and Informatics (RBVI), UCSF |
| Aktuelle Version | 1.4 (3. Dezember 2009) |
| Betriebssystem | Windows, Mac OS X, Linux, und andere |
| Kategorie | Simulationssoftware |
| Lizenz | kostenlos für nicht-kommerziellen Einsatz |
| deutschsprachig | nein |
| www.cgl.ucsf.edu/chimera | |
UCSF Chimera (oder einfach Chimera) ist ein erweiterbares Programm für die interaktive Darstellung und Analyse von molekularen Strukturen und damit verbundenen Daten, z.B. Sequenzalignments, Resultaten aus Docking-Experimenten, Elektronendichtekarten und weiteren Anwendungen. Mit dem Programm können qualitativ hochwertige Bilder und Animationen angefertigt werden. Für nicht-kommerzielle Anwendungen kann Chimera kostenlos herunter geladen und verwendet werden.
Chimera wird durch die Resource for Biocomputing, Visualization, and Informatics (RBVI) an der University of California, San Francisco entwickelt.
Allgemeine Struktur Analyse
[Bearbeiten | Quelltext bearbeiten]- Automatische Indentifikaton der verschiedenen Atomtypen
- Hinzufügen von Wasserstoffatomen und teilweise Zuordnung von Ladungen
- Qualitativ hochwertiges Auffinden von Wasserstoffbrücken, Kontakten und Konflikten innerhalb der Strukturen
- Messungen der Entfernungen und Winkel zwischen Atomen
- Erkennung von frei drehbaren Bindungen
- Rotamer Datenbank für Aminosäuren (Rückgrat-abhängig und -unabhängig)
- Wiedergabe der Bewegungsbahnen (Trajektorien) von molekularen Dynamiken in verschiedenen Formaten
- clustering of conformational ensembles
- morphing between conformations of a protein or even different proteins
- display of attributes (B-factor, hydrophobicity, etc.) with colors, radii, "worms"
- easy creation of new attributes with simple text file inputs
- rich set of commands, powerful specification syntax
- many formats read, PDB and Mol2 written
- web fetch from Protein Data Bank, PQS (predicted quaternary structure), CASTp (protein pocket measurements), EDS (density maps), ModBase (comparative models), Pub3D (small molecule structures), others
Presentation Images and Movies
[Bearbeiten | Quelltext bearbeiten]- images can be saved at arbitrarily high resolution
- adjustable background color, lighting, depth-cueing, silhouette edges
- stick, ball-and-stick, sphere, ribbon, and surface displays
- nonmolecular geometric objects
- labeling with arbitrary text and symbols, color keys
- isosurfaces and transparent renderings of volume data (see below)
- different structures can be clipped differently and at any angle
- optional raytracing with bundled POV-Ray
- scene export to X3D and other formats
- simple graphical interface for creating movies interactively
- alternatively, movie content and recording can be scripted
- movie recording is integrated with morphing and MD trajectory playback
Volume Data Tools
[Bearbeiten | Quelltext bearbeiten]- many formats of volume data maps (electron density, electrostatic potential, others) read, several written
- interactive threshold adjustment, multiple isosurfaces (mesh or solid), transparent renderings
- fitting of atomic coordinates to maps and maps to maps
- density maps can be created from atomic coordinates
- markers can be placed in maps and connected with smooth paths
- display of single data planes, optionally as topographic maps
- volume data time series playback and morphing
- many tools for segmenting and editing maps
- Gaussian smoothing, Fourier transform
- surface area and surface-enclosed volume measurements
Sequence and Structure Tools
[Bearbeiten | Quelltext bearbeiten]- many sequence alignment formats read, edited, written
- Newick tree format read
- automatic, mismatch-tolerant association of structures with alignment sequences
- sequence-structure crosstalk: highlighting in one highlights the other
- multiple methods for calculating conservation and displaying values on associated structures
- structure superposition using the associated sequence alignment
- in the absence of a pre-existing alignment, structure superposition using both residue type and secondary structure information
- generation of structure-based sequence alignments from superpositions of two or more proteins
See also
[Bearbeiten | Quelltext bearbeiten]- List of molecular graphics systems
- Molecular modelling
- Molecular graphics
- Molecular dynamics
- Software for molecular mechanics modeling
External links
[Bearbeiten | Quelltext bearbeiten]- UCSF Chimera home page
- Chimera Image Gallery and Animation Gallery
- papers about Chimera
- Resource for Biocomputing, Visualization, and Informatics
- University of California, San Francisco
[[Category:Molecular modelling software]] [[Category:Bioinformatics software]] [[Category:Science software]] [[Category:Freeware]]
Erledigtes
[Bearbeiten | Quelltext bearbeiten]Pflanzenarten
[Bearbeiten | Quelltext bearbeiten]Zu Flora Australiens
Alte Version