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.

Assemble2: design RNA structure in 2D, build in 3D

Dec 18, 2012

Assemble2 allows designing 2D RNA structures interactively and generating corresponding 3D structures in Chimera. It uses web services for RNA structure prediction and refinement. Executables, source code, and documentation are available for download. Assemble2 is developed by Fabrice Jossinet at the Institut de Biologie Moléculaire et Cellulaire, Strasbourg.

SwissSidechain: non-natural amino acids

Dec 1, 2011

The SwissSidechain Chimera module allows mutating amino acids into non-natural residues found in the SwissSidechain database, using a Rotamers-type interface or an additional command, swapnaa. The database includes rotamers for > 200 non-natural residues (browse...). The module and database are developed by David Gfeller, Olivier Michielin, and Vincent Zoete in the Swiss Institute of Bioinformatics Molecular Modelling Group.


ViewDock TDW: Visualization of Virtual Screening Results on Tiled Display Walls

May 5, 2010

The ViewDock TDW extension allows visualization and modification of DOCK screening results using Tiled Display Walls. Developed by Christopher Lau in collaboration with Dr. Jason Haga at UCSD and Dr. Susumu Date at Osaka University (see credits).


Viewer for psc++-calculated pairwise/multiple alignments

July 27, 2009

PscViewer facilitates the calculation and visualization of pairwise and multiple structure-based alignments. PscViewer is mainly an interface to the psc++ structure alignment program but also supports display of structure alignments if specified in a certain XML-based format. PscViewer contains three tools:

  1. Create/View Psc++ Alignment to calculate and view alignments.
  2. Load XML file to load and display precalculated alignments stored in a certain XML format.
  3. Load Database Search to load a ranked list of hist in a structure database given a certain query and subsequently to calculate the corresponding pairwise alignment. The ranked list data can be derived with psc++.

Developed by Wolfgang Skala at the University of Salzburg.

Viewer for 3D motif matches from LabelHash

April 24, 2009

The LabelHash 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. LabelHash and ViewMatch are provided by the Kavraki Lab at Rice University.

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 connects Chimera to the Structure-Based Local Environment Search Tool (S-BLEST), which uses vectors of amino acid structural environments to perform K Nearest Neighbor queries against a database of protein structures. Developed by the Mooney lab.

Show single nucleotide polymorphisms (SNPs)

April 3, 2007

The MutDB extension shows locations of SNPs in structures using data from MutDB. Developed by the Mooney lab.

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 web service for functional analysis of protein structures using residue environments. Developed by the Mooney lab.

Molecular orbital properties

April 3, 2007

The AOMix molecular orbital analysis package can output Chimera attribute files listing charges, MPA and LPA spin densities, and total and free valence indices. No plug-in is required to assign and view the resulting attributes in Chimera. Developed by Serge Gorelsky.

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 in the Babbitt lab 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.