Exporting a Scene

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

POV-Ray, RenderMan, STL, and VRML files are generated by postprocessing an initial X3D file. The conversion programs x3d2pov, x3d2RM, x3d2stl, and x3d2vrml are included with Chimera (in the bin directory) but can be used separately.

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, global clipping, 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.

The VRML and X3D outputs do not support: RenderMan supports depth cueing and clipping planes; otherwise, limitations are as listed above for VRML and X3D.

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.

UCSF Computer Graphics Laboratory / March 2023