Experimental Chimera Features

These experimental features may be included in a future Chimera release. You can download them here and use them as plug-ins with your already installed Chimera.

Export Surfaces in Wavefront OBJ format

Export volume contour surfaces, multiscale surfaces, molecular surfaces and others in Wavefront OBJ format for input into animation packages.

Included in Chimera version 1.2485, using menu File / Export Scene.

July 27, 2005, exportobj.zip. Installation. Details.
Tested with Chimera version 1.2470.

POV-Ray Blobs

Tool and command to render displayed atoms as POV-Ray blobs which are defined as "iso-surfaces of scalar fields."

April 25, 2007, povblob.zip. Installation. Details.
Tested with Chimera version 1.2382.

Resample Map Commands

Commands to extract pieces of density maps with axes not aligned with the original map. Values are interpolated (i.e. resampled) on a new grid.

Equivalent capability available in Chimera version 1.2443, using Volume Viewer subregion selection panel.

March 13, 2007, resamplemap.zip. Installation. Details.
Tested with Chimera version 1.2352. Does not work with versions newer than 1.2430.

Morph Map

Linearly interpolates pointwise between two volume data sets and creates animations changing one map into another.

Morph map included in Chimera version 1.2456.

February 27, 2007, morphmap.zip. Installation. Details. Older versions.
Requires Chimera version 1.2348 or newer.

Transform Molecule Coordinates

Applies a rotation and translation to atom coordinates with the rotation specified in Euler angles.

Included in Chimera version 1.2456.

January 30, 2007, moltransform.zip. Installation. Details.
Tested with Chimera version 1.2304.

Crystal Coordinates

Python script to write PDB coordinates for a block of crystal unit cells.

January 12, 2007, crystalcoords.zip. Details and Use.
Tested with Chimera version 1.2304.

QPACK Interface

Tool to invoke QPACK for evaluation of packing in protein structures.

January 11, 2007, qpack.zip. Installation. Details.
Tested with Chimera version 1.2332.

Volume Plane Display

Display planes of a volume data set perpendicular to the z-axis. Provides a slider to select which z-plane to display.

Equivalent capability available in Chimera version 1.2430, using Volume Viewer planes panel.

December 11, 2006, volumeplanes.zip. Installation. Details.
Tested with Chimera version 1.2309. Does not work with versions newer than 1.2440.

Mesh with Cylindrical Lines

Command to make a molecule model from a surface mesh in order to display the mesh using cylindrical line segments. Mesh can be saved as a PDB file.

Included in Chimera version 1.2456.

November 28, 2006, meshmol.zip. Installation. Details.
Tested with Chimera version 1.2309.

Gaussian Filter

Improve signal to noise and reduce resolution of volume data by convolving with a Gaussian.

Gaussian filter included in Chimera version 1.2454.

October 10, 2006, gaussianfilter.zip. Installation. Details. Older versions.
Requires Chimera version 1.2348 or newer.

Icosahedral Cage Command

Adds hkcage command to display hexagonal mesh on an icosahedron. Illustrates arrangement of proteins on a virus capsid.

Included in Chimera version 1.2456.

October 2, 2006, hkcage.zip. Installation. Details. Older versions.
Requires Chimera version 1.2348 or newer.

IMOD File Reader

Read IMOD binary files containing segmented objects from 3-dimensional microscopy data.

IMOD file reader included in Chimera version 1.2454.

May 11, 2007, imod.zip. Installation. Details. Older versions.
Requires Chimera version 1.2348 or newer.

Distance to Surface

Report the distance from atoms or markers to displayed surfaces.

Included in Chimera version 1.2456.

September 5, 2006, surfdist.zip. Installation. Details.
Tested with Chimera version 1.2255.

Split Volume by Color Zone

Split a volume data set into multiple data sets, one for each distinct color in a coloring done by the Color Zone tool.

Split volume included in Chimera version 1.2454.

September 1, 2006, splitmap.zip. Installation. Details. Older versions.
Requires Chimera version 1.2348 or newer.

Crystal Contacts

Display contacts between asymmetric units of crystals.

Included in Chimera version 1.2456.

August 8, 2006, crystalcontacts.zip. Installation. Details. Older versions.
Requires Chimera version 1.2348 or newer.

Virus EM Map Images

Generate images for sets of virus density maps.

October 17, 2006, viperem.zip. Use. Older versions.
Requires Chimera version 1.2348 or newer.

Set Magnification and Window Size

Commands to set absolute magnification in pixels per angstrom and window size in pixels.

The windowsize command is included in Chimera version 1.2314 and newer.

May 2, 2006, zoom.zip. Installation. Details.
Tested with Chimera version 1.2199.

Volume Series

Displays sequences of volume data sets such as 3D optical microscopy time series.

Included in Chimera version 1.2456.

August 2, 2006, volumeseries.zip. Installation. Details. Older versions.
Requires Chimera version 1.2348 or newer.

Movement Mouse Mode

Allows moving helices, strands, turns, PDB chains, any selected set of atoms, or multiscale model chains with the mouse. Improved version of earlier "move selected atoms" tool.

Included in Chimera version 1.2456.

April 7, 2006, movemode.zip. Installation. Details.
Requires Chimera version 1.2206 or newer.

Nucleic Acid Blobs

Depict nucleic acid backbones and bases using separate surfaces.

April 5, 2006, reschains.py. Installation. Details.
Tested with Chimera version 1.2199.

Flatten Icosahedron

Flattens viral capsid multiscale models into a plane.

Included in Chimera version 1.2456.

June 14, 2006, flattenicosahedron.zip. Installation. Details. Older versions.
Requires Chimera version 1.2348 or newer.

Split Molecule Command

Makes chains of a molecule into separate molecules.

Included in Chimera version 1.2456.

April 10, 2006, splitmolecule.zip. Installation. Details.
Tested with Chimera version 1.2199.

Multiscale Coloring Command

Color multiscale models to match atom colors.

Included in Chimera version 1.2456.

January 11, 2006, multiscalecolor.zip. Installation. Details.
Requires Chimera version 1.2197. Older Chimera versions will not work.

Animation Commands

Miscellaneous animation commands. Vary volume data contour level. Make multiscale protein surfaces fly away radially. Smoothly change radius in icosahedral surface tool.

September 21, 2007, transition.zip. Installation. Details. Older versions.
Requires Chimera version 1.2470 or newer.

Color and Measure Surface Pieces

Tool to color and measure the enclosed volume of disjoint pieces of volume contour surfaces.

Included in Chimera version 1.2456.

November 17, 2006, pickblobs.zip. Installation. Details. Older versions.
Requires Chimera version 1.2348 or newer.

Symmetric Molecule Copies

Command to create symmetric copies of a PDB model using BIOMT REMARK matrices and maintain the symmetry as one copy is positioned with the mouse in a density map.

Included in Chimera version 1.2456.

November 6, 2006, symmetrycopies.zip. Installation. Details.
Tested with Chimera version 1.2172.