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.
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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