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.
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Export Surfaces in Wavefront OBJ formatExport 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. |
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POV-Ray BlobsTool 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. |
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Resample Map CommandsCommands 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. |
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Morph MapLinearly 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. |
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Transform Molecule CoordinatesApplies 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. |
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Crystal CoordinatesPython script to write PDB coordinates for a block of crystal unit cells.
January 12, 2007,
crystalcoords.zip.
Details and Use. |
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QPACK InterfaceTool to invoke QPACK for evaluation of packing in protein structures.
January 11, 2007,
qpack.zip.
Installation.
Details. |
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Volume Plane DisplayDisplay 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. |
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Mesh with Cylindrical LinesCommand 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. |
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Gaussian FilterImprove 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. |
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Icosahedral Cage CommandAdds 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. |
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IMOD File ReaderRead 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. |
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Distance to SurfaceReport the distance from atoms or markers to displayed surfaces. Included in Chimera version 1.2456.
September 5, 2006,
surfdist.zip.
Installation.
Details. |
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Split Volume by Color ZoneSplit 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. |
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Crystal ContactsDisplay contacts between asymmetric units of crystals. Included in Chimera version 1.2456.
August 8, 2006,
crystalcontacts.zip.
Installation.
Details.
Older versions. |
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Virus EM Map ImagesGenerate images for sets of virus density maps.
October 17, 2006,
viperem.zip.
Use.
Older versions. |
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Set Magnification and Window SizeCommands 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. |
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Volume SeriesDisplays 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. |
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Movement Mouse ModeAllows 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. |
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Nucleic Acid BlobsDepict nucleic acid backbones and bases using separate surfaces.
April 5, 2006,
reschains.py.
Installation.
Details. |
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Flatten IcosahedronFlattens viral capsid multiscale models into a plane. Included in Chimera version 1.2456.
June 14, 2006,
flattenicosahedron.zip.
Installation.
Details.
Older versions. |
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Split Molecule CommandMakes chains of a molecule into separate molecules. Included in Chimera version 1.2456.
April 10, 2006,
splitmolecule.zip.
Installation.
Details. |
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Multiscale Coloring CommandColor multiscale models to match atom colors. Included in Chimera version 1.2456.
January 11, 2006,
multiscalecolor.zip.
Installation.
Details. |
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Animation CommandsMiscellaneous 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. |
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Color and Measure Surface PiecesTool 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. |
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Symmetric Molecule CopiesCommand 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. |