This site contains 3D density maps obtained by electron microscopy in CCP4 format that can be shown with Chimera Volume Viewer.
See also: Web services used by UCSF Chimera, sites that provide Chimera Web data, and Chimera plug-ins on the Web
ASTRAL
Experimentally determined protein structures, divided into domains
as defined by
SCOP
(Structural Classification of Proteins).
Conformational Dynamics Data Bank
Provides conformational dynamics of proteins and protein assemblies from
normal mode analysis. CDDB uses Chimera to compute and export surface mesh;
data files include density maps that can be viewed in Chimera.
Cube-DB Database of pre-evaluated conservation and specialization scores for multi-member families of human proteins. Includes downloadable Chimera session files with color-coded structures. Cube-DB is described in Zhang et al., Nucleic Acids Res 40:D490 (2012).
Database
for Aligned Ribosomal Complexes (DARC)
Ribosomal structures from the PDB and EMDB aligned into a common frame
of reference. Data processed with Chimera, can be viewed with Chimera.
DARC is described in
Jarasch
et al., Nucleic Acids Res 40:D495 (2012).
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This site contains 3D density maps obtained by electron microscopy in CCP4 format that can be shown with Chimera Volume Viewer. |
EM Navigator
Presents images, movies, Chimera sessions and details about electron microscopy
density maps from the EM DataBank.
Insulin-like
Growth Factor Mutation Database
Searchable/browsable repository of IGF mutants and associated
receptor-binding data; mutations mapped to structure in Chimera images.
LS-SNP/PDB
A database of human nonsynonymous single-nucleotide
polymorphisms (nsSNPs) mapped onto protein structures.
Chimera-generated images show SNP locations in the structures and
molecular surfaces colored by superfamily sequence conservation and
DelPhi-computed electrostatic potential.
ModBase
A database of three-dimensional protein models calculated by
comparative modeling.
Mutagenetix
A database of mouse mutations and phenotypes induced by ENU.
Many of the allele pages include molecular structure images and
movies made in Chimera.
MutDB
A database that associates human SNP and mutation data with
protein structures. The authors
provide
a Chimera extension to access the data via web services.
PhosphoSitePlus
Comprehensive information and tools for the study of protein
post-translational modifications; includes scripts for visualization
in Chimera.
Protein Data Bank (PDB)
Experimentally determined protein and nucleic acid structures.
Display PDB format files.
Structure Function Linkage Database
Connecting enzyme structure and function at the level of conserved
partial chemical reactions.
UCSC Genome Browser
Chimera links are provided in UCSC Gene pages
(see example) and SNP track details pages.
Clicking a Chimera link displays the corresponding structure
with nonsynonymous SNP residues colored and
labeled with the dbSNP identifier.
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Crystallographic electron density maps for protein data bank x-ray structures. Display O, CCP4, or CNS format density maps with Chimera Volume Viewer. |
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Atomic resolution virus capsid structures. Some of the capsid images on this site are made with the Chimera Multiscale Models tool. |
Amber
Molecular force field and dynamics simulations.
Display trajectories with the Chimera
MD Movie extension.
Box Beam Backbone Sculptures
Design protein backbone sculptures made from metal box beams or wood.
ConSurf Server
Given a query structure, the server finds related sequences, aligns them,
and displays conservation on the structure.
Clicking the link to view results in Chimera uses the
Chimera web data mechanism to display the structure and
sequence alignment colored by conservation, as well as the
ConSurf-calculated phylogenetic tree and custom alignment headers
(example).
deconSTRUCT
Server
The server can compare two structures or search the PDB
for structures similar to a query. The resulting pairwise superpositions
can be viewed in Jmol and downloaded in various forms,
including Chimera sessions.
DOCK
Given 3D structures of molecules, DOCK addresses the problem of how they
might fit or bind together. Using Chimera, one can:
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For reconstructing 3d models from a set of randomly oriented particle images. EMAN includes the EMANimator extension for making animations in Chimera, focused on volume data. |
LabelHash Server
The server searches the PDB for matches to a user-specified
3D motif (pattern of residues). The authors provide the Chimera extension
ViewMatch
for looking through the hits superimposed on the query.
LabelHash can also be
downloaded
for local command-line use.
MoSuMo MoSuMo is a Semantic Web service for generating electrostatic potentials mapped to molecular surfaces. It requires the headless version of Chimera (Linux). MoSuMo can be downloaded from the Dumontier Lab, Carleton University, and is described in Gawronski and Dumontier, Comput Graph 35:823 (2011).
Pfinder
The Pfinder program predicts phosphate-binding sites in protein structures.
It requires the headless version of Chimera (Linux). Pfinder can be
downloaded
from the Centre for Molecular Bioinformatics, University of Rome,
and is described in
Parca
et al., Nucleic Acids Res 39:1231 (2011).
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The Ringer program detects molecular motions by systematically sampling X-ray electron density; the aim is to go beyond static structural snapshots of proteins by uncovering structural ensembles. The program depends on Chimera. Ringer is available from the Alber lab at UC Berkeley, and is described in Lang et al., Protein Sci 19:1420 (2010). |
Sparky
Assignment of NMR spectra for determining protein and nucleic acid structures.
Uses Chimera to
display NMR peak assignments
on a molecular model.
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A plugin to Cytoscape that integrates visualization and analysis of protein networks or pathways in Cytoscape with visualization and analysis of corresponding structures in Chimera. |
RINalyzer
A Java plugin to Cytoscape
that integrates 2D visualization of residue interaction networks
(RINs) in Cytoscape with 3D visualization of corresponding
structures in Chimera.
Computational Chemistry List (ccl.net)
PDB Discussion Forum (pdb-l@rcsb.org)