This site contains 3D density maps obtained by electron microscopy, and other data. All entries. Search. Details. Display CCP4 format density maps with Chimera Volume Viewer.
See also: Web services used by UCSF Chimera and Chimera Plug-ins on the Web
ASTRAL
Experimentally determined protein structures, divided into domains
as defined by
SCOP
(Structural Classification of Proteins).
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.
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This site contains 3D density maps obtained by electron microscopy, and other data. All entries. Search. Details. Display CCP4 format density maps with Chimera Volume Viewer. |
ModBase
A database of three-dimensional protein models calculated by
comparative modeling.
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.
Protein Data Bank
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.
Structure Superposition Database
For accessing, viewing, and understanding large sets of structure
superposition data. The
SSD user interface
is a Chimera extension.
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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.
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).
DOCK
DOCK addresses the problem of "docking" molecules to each other.
It explores ways in which two molecules, such as a drug and an enzyme or
protein receptor, might fit together.
Screen DOCK results with the Chimera
ViewDock extension. View scoring grids with
Volume Viewer.
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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. It also includes the Isosurface Colorizer extension (undocumented) to radially color density maps, or color one map using a second map. |
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.
Sparky
Assignment of NMR spectra for determining protein and nucleic acid structures.
Uses Chimera to
display NMR peak assignments
on a molecular model.
Computational Chemistry List (ccl.net)
PDB Discussion Forum (pdb-l@rcsb.org)