Crystallographic packing can also be shown. Matrices are read from PDB files that specify the biological unit. It displays the quaternary structure of Protein Data Bank (PDB) models and allows subunits to be selected and shown in atomic detail. Multiscale Models - The Multiscale Models extension allows Chimera to display large complexes such as virus capsids, ribosomes, and chromatin. Markers can be placed and structures can be traced. Maps can be colored, sliced, segmented, and modifications can be saved. Contour surfaces, meshes and volumetric display styles are provided and thresholds can be changed interactively. Volume Data - Chimera's “Volume Viewer” displays three-dimensional electron and light microscope data, X-ray density maps, electrostatic potential and other volumetric data. Showing ConSurf Results - The ConSurf Server provides results as Chimera Web data after browser configuration, a single click displays the color-coded query structure and multiple sequence alignment with phylogenetic tree and custom headers in a locally installed copy of Chimera. d) Selection of atoms/bonds by element, atom type, functional group, amino acid category and interactive bond rotation, distance and angle measurements.c) High-quality hydrogen bond identification.a) Determination of atom types in arbitrary molecules, including non-standard residues.f) ability to save high-resolution images for presentation and publication and stereo (side-by-side and time-sequential).e) Interactive color editing in various color spaces (RGB, CMYK, etc.) with transparency and.d) Side View for adjusting clipping planes and scaling.c) Highly intuitive rotation, translation, and scaling with the mouse.a) Stick, ball-and-stick, CPK, ribbon, pipe-and-plank, and nucleotide display styles.The morph can then be saved in coordinate form or recorded as an animation. The result is displayed in Chimera’s trajectory viewer, MD Movie (MD Movie - is a tool for viewing and analysis of trajectories and other ensembles). Users can specify the method of coordinate interpolation and how many intermediate structures should be generated. Morphing - Different conformations and even different proteins can be compared, by morphing from one structure to another. Secondary structure elements can be depicted as colored boxes or regions on the alignment. Various measures of sequence conservation and structural variation (RMSD) can be computed and shown above the sequences as histograms, and on the structures with color or worm radius. Structures opened in Chimera are automatically associated with sufficiently similar sequences in the alignment.Īfter association, mousing over a residue in the sequence shows its structure residue number, selecting in the sequence selects residues in the structure(s) and vice versa, structures can be superimposed using sequence alignment. Sequence alignments can be read from external files or created by other tools in Chimera. Sequence Viewer - The “Multalign Viewer” tool displays individual sequences and multiple sequence alignments. High-quality images and animations can be generated. It can be used for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. Category Proteomics>Protein Structure/Modeling Systems/ToolsĪbstract UCSF Chimera is an molecular modeling system.
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