Chimera Plug-ins on the Web

These are Chimera plug-ins developed and distributed by other groups. More plug-ins are available on the Chimera experimental features page.

Slice viewer for electron tomography April 3, 2007 TomoPlane displays slices of electron tomography data sets oriented at arbitrary angles. Developed by Karin Gross and Christoph Best at Max Planck Institute for Biochemistry.

Predict non-linear optical properties of molecules April 3, 2007 NLOPredict predicts and analyze non-linear optical properties of molecules. Developed by in a collaboration between the lab of Prof. Garth Simpson at Purdue University and Charlie Moad and Randy Heiland at the Scientific Data Analysis Lab, a Pervasive Technology Lab of Indiana University.

Analysis tools for high resolution electron cryo-microscopy April 3, 2007 The Analysis of Intermediate Resolution Structures (AIRS) toolkit is designed for structure discovery in intermediate resolution structures from electron cryomicroscopy. AIRS contains tools for filtering, segmentation, analysis and docking, in addition to a variety of other visualization tools. Developed by Matthew Baker (mbaker@bcm.tmc.edu) at Baylor College of Medicine.

Animation Editor April 3, 2007 EMANimator creates animations of electron microscope maps and molecular models using a graphical timeline interface. Supports model motions, model color changes, showing and hiding models, changing thresholds for isosurfaces, and camera zooms. Developed by Steve Ludtke at Baylor College of Medicine.

Find proteins having similar sites April 3, 2007 The SBlest interface uses vectors of amino acid structural environments to perform K Nearest Neighbor queries against a database of protein structures. This is an interface to the Structure-Based Local Environment Search Tool (S-BLEST). Developed by the Sean Mooney lab at Indiana University.

Show single nucleotide polymorphisms (SNPs) April 3, 2007 The MutDB extension shows locations of SNPs in structures using data from MutDB. Developed by the Sean Mooney lab at Indiana University.

Catalytic site prediction web service April 3, 2007 The Catalytic Site Prediction tool included in the LSW Clients package of Chimera extensions provides an interface to an S-BLEST database web service for identifying catalytic sites. Developed by the Sean Mooney lab at Indiana University.

Molecular orbital properties April 3, 2007 The AOMix molecular orbital analysis package can output Chimera atom attribute files listing charges, MPA and LPA spin densities, and total and free valence indices. No plug-in is required to view these files in Chimera. Developed by the Serge Gorelsky lab at Stanford University.

Analyze microenvironments around protein sites April 3, 2007 The ViewFeature extension enables visualization of distinguishing properties in a 3-D structure within specified volumes, giving users insight into the structural motifs that define a given site. Developed by D. Rey Banatao in the Helix Group at Stanford University.

User interface to Structure Superposition Database April 3, 2007 Using the SSD extension, users can view all or a subset of the superpositions for a given pair of structures, view multiple structure superpositions, access RMSD values and other quantities describing the superpositions, and view pairwise and multiple sequence alignments derived from the structural superpositions. Developed by Ranyee Chiang at the University of California at San Francisco.

View NMR assignments on a molecular structure April 3, 2007 The Sparky molecule view extension displays NMR assignments and distance constraints from the NMR assignment program Sparky on a molecular structure. Developed by Tom Goddard at the University of California at San Francisco.