Hello Developers, In the recent chimera release candidates and the imminent 1.2180 production release, there several API changes that may trip up existing code. Many of these changes are due to our improved method of moving data between Python and the underlying C++ layer (roughly 2X faster). Most of the changes are detailed below. Greg Couch gregc@cgl.ucsf.edu ------ The new code works much better with the Python help function. In the IDLE window, try help(chimera.Atom) and you'll see all of Atom's methods and their argument types and return values. For the changes below assume: m is a Molecule r is a Residue a is an Atom b is a Bond x is a Xform Atoms have a simpified interface to their bonds: a.bonds() returns a list of bonds a.neighbors() returns a list of adjacent atoms (via bonds) a.bondsMap() is both of the above combined as a dictionary and is what a.bonds() used to return If a structure has alternate locations, you can get just the highest occupancy bonds/atoms with a.primaryBonds() and a.primaryNeighbors(). Molecules have a corresponding m.primaryAtoms() function. Residues have a simpified interface to their atoms: r.atoms() returns a list of atoms r.atomNames() returns a list of atom names r.atomsMap() is both of the above combined as a dictionary with atom name as the key and a list of atoms with that name as the value Residue ids (of type MolResId) no longer have an exposed str method: r.id.str() is now 'str(r.id)' or 'print r.id' MolResId, Point, Vector, and Xform now have copy constructors. You can make copies in the C++ style, 'xprime = Xform(x)', or in the Python style with the copy module or the __copy__ method. The following chimera module functions are now static methods: Atom_getIdatmInfoMap -> Atom.getIdatmInfoMap Camera_hasMode -> Camera.hasMode Camera_modes -> Camera.modes Color_list -> Color.list Color_lookup -> Color.lookup Color_remove** Element_bondLength -> Element.bondLength Element_bondRadius -> Element.bondRadius LODControl_get -> LODControl.get Material_list -> Material.list Material_lookup -> Material.lookup Material_remove** Mol2io_isBlankLine -> Mol2io.isBlankLine Mol2io_splitLine -> Mol2io.splitLine OGLFont_defaultFont -> OGLFont.defaultFont OGLFont_setDefaultFont -> OGLFont.setDefaultFont OpenModels_get -> OpenModels.get PDBio_addStandardResidue -> PDBio.addStandardResidue PDBio_bondLengthTolerance -> PDBio.bondLengthTolerance PDBio_removeStandardResidue -> PDBio.removeStandardResidue PDBio_setBondLengthTolerance -> PDBio.setBondLengthTolerance PDBio_standardResidue -> PDBio.standardResidue PixelMap_list -> PixelMap.list PixelMap_lookup -> PixelMap.lookup PixelMap_maxLength -> PixelMap.maxLength PixelMap_remove** PseudoBondMgr_mgr -> PseudoBondMgr.mgr Residue_getDefaultRibbonStyle -> Residue.getDefaultRibbonStyle RibbonResidueClass_classes -> RibbonResidueClass.classes RibbonResidueClass_deregisterClass -> RibbonResidueClass.deregisterClass RibbonResidueClass_registerClass -> RibbonResidueClass.registerClass RibbonXSection_circle -> RibbonXSection.circle RibbonXSection_line -> RibbonXSection.line RibbonXSection_square -> RibbonXSection.square Selectable_count -> Selectable.count Shader_list -> Shader.list Shader_lookup -> Shader.lookup Shader_remove** Spline_makeGeometryVector -> Spline.makeGeometryVector Texture_computeComponents -> Texture.computeComponents Texture_computeDimension -> Texture.computeDimension Texture_computeImageTypeBytes -> Texture.computeImageTypeBytes Texture_computeTarget -> Texture.computeTarget Texture_list -> Texture.list Texture_lookup -> Texture.lookup Texture_remove** TrackChanges_get -> TrackChanges.get Xform_coordFrame -> Xform.coordFrame Xform_identity -> Xform.identity Xform_lookAt -> Xform.lookAt Xform_rotation -> Xform.rotation Xform_translation -> Xform.translation Xform_xRotation -> Xform.xRotation Xform_xform -> Xform.xform Xform_yRotation -> Xform.yRotation Xform_zAlign -> Xform.zAlign Xform_zRotation -> Xform.zRotation ** Color_remove, Material_remove, PixelMap_remove, Shader_remove, and Texture_remove Unlike C++, Python can not have a method and a static method with the same name. So the static method versions have been excised from the Python layer.