Exporting a Scene

File... Export Scene allows a description of the Chimera scene to be saved in the following formats:

• ChimeraX [.py] **under development** - Python file for regenerating the scene in ChimeraX (currently includes atomic models, molecular surfaces, sequences and sequence alignments, 2D labels, and color key, but not volume models, other surface models, etc.)
• COLLADA [.dae] - COLLADA XML-based format; can be viewed with Mac Preview and incorporated into iBooks
• OBJ [.obj] - Wavefront OBJ (surfaces only); colors are written to a separate material definition file [.mtl]
• POV-Ray [.pov] - input for the Persistence of Vision Raytracer
  (alternatively, POV-Ray images can be produced directly)
• RenderMan [.rib] - RenderMan^® Interface Bytestream
• STL [.stl] - triangle-based format (binary) native to stereolithography CAD software (see the Chimera 3D Model Gallery)
• VRML [.wrl, .vrml] - Virtual Reality Markup Language
• VTK [.vtk] - format used by Visualization Toolkit
• WebGL [.html] - HTML5 format with embedded WebGL, to show a manipulable rendering of the scene in a web page (experimental feature)
• X3D [.x3d]

Only what is displayed will be exported. Note that something can be displayed yet invisible due to clipping or zoning, or because it simply falls outside the current view.

See also: saving data, export, struts, save, write, copy, Write DMS, Animation storyboard, raytracing with POV-Ray, tips on preparing images

The COLLADA export does not support text, silhouettes, or per-model clipping. It has been tested mainly on Macs, with proper rendering observed in Preview (Mac 10.8) and iBooks on iPad. Other applications (e.g. SketchUp and MeshLab tested on Windows) correctly handle the geometry but not the triangle vertex colors.

Exports to OBJ format only include displayed surface models. The entire surfaces (even if only partially displayed) are exported in their untransformed positions. Only a single color is exported per surface piece.

A raytraced image from POV-Ray may differ from the view in Chimera in several ways.

• depth cueing
• global clipping (X3D supports per-model clipping, VRML does not)
• stereo
• Volume Viewer transparent solid displays
• normals on dot and mesh surfaces

STL does not include color, dots, lines, or text, in addition to sharing the limitations listed above for VRML and X3D.

VRML does not support variations in transparency within a single surface model; different surface models can have different transparencies, but for a given surface model, the transparency of its least transparent point will be used.

VTK export includes only molecule models, molecular surfaces, and multiscale surfaces with associated atoms. The molecule export includes all atoms and bonds, even if not displayed, and uses dots to represent atoms and wires to represent bonds regardless of their display styles in Chimera. The atoms have VTK attributes including model number, atom index, residue type, residue index, atom name, bfactor and occupancy. Each surface vertex also has this same set of attributes for the nearest atom. The atom index and residue index are simply the positions in the lists of atoms and residues, respectively, not the atom serial number or residue number in Chimera.

WebGL export is an experimental feature.

X3D viewers and plugins are available for some platforms, but this format is relatively new and continues to evolve. Annotations for clipping planes and depth cueing can be included in the file even though these features are not displayed.