| 1 | = Molecule graphics attributes for Chimera 2, based on Chimera 1 = |
| 2 | "*" indicates something we may change in Chimera 2. |
| 3 | |
| 4 | == Atom == |
| 5 | |
| 6 | display (true/false) |
| 7 | |
| 8 | hide (true/false, is atom shown when ribbon style shown) |
| 9 | |
| 10 | drawMode (Dot, Sphere, EndCap, Ball) |
| 11 | |
| 12 | color |
| 13 | |
| 14 | |
| 15 | label (text string for 3d label) |
| 16 | |
| 17 | labelOffset (xyz position relative to atom) |
| 18 | |
| 19 | labelColor |
| 20 | |
| 21 | minimumLabelRadius |
| 22 | |
| 23 | |
| 24 | *surfaceDisplay (drop this, visibility of surface per-atom) |
| 25 | |
| 26 | *surfaceColor (drop this, used for color by atom, instead have surface remember this mapping) |
| 27 | |
| 28 | *surfaceOpacity (drop this, used for color by atom) |
| 29 | |
| 30 | *surfaceCategory (drop this? categories will be like other named selectors?) |
| 31 | |
| 32 | |
| 33 | *vdwPoints (drop this) |
| 34 | |
| 35 | *vdwColor (drop this) |
| 36 | |
| 37 | *Thermal ellipsoids for atoms -- in Python in Chimera 1 |
| 38 | |
| 39 | scaleFactor (float, scales size) |
| 40 | |
| 41 | probabilityLevelForScaling (percentage) |
| 42 | |
| 43 | smoothingLevel (level of detail for ellipsoid) |
| 44 | |
| 45 | displayEllipsoid (true/false) |
| 46 | |
| 47 | displayPrincipalAxes (true/false, show lines for ellipsoid axes) |
| 48 | |
| 49 | axesLengthFactor (flaot) |
| 50 | |
| 51 | axesThickness (float) |
| 52 | |
| 53 | displayPrincipalEllipses (true/false, show orthogonal planes of ellipsoid) |
| 54 | |
| 55 | ellipsesSizeFactor (float) |
| 56 | |
| 57 | ellipsesThickness (float) |
| 58 | |
| 59 | == Bond == |
| 60 | display (true/false) |
| 61 | |
| 62 | drawMode (wire, stick, spring) |
| 63 | radius |
| 64 | |
| 65 | color |
| 66 | halfbond (color each half of bond to match near atom) |
| 67 | |
| 68 | label (text) |
| 69 | labelColor |
| 70 | labelOffset (xyz position relative to bond center) |
| 71 | |
| 72 | == PseudoBond (same attributes as Bond) == |
| 73 | display (true/false) |
| 74 | |
| 75 | drawMode (wire, stick, spring) |
| 76 | radius |
| 77 | |
| 78 | color |
| 79 | halfBond (color each half of bond to match near atom) |
| 80 | |
| 81 | label (text) |
| 82 | labelColor |
| 83 | labelOffset (xyz position relative to bond center) |
| 84 | |
| 85 | == Residue == |
| 86 | ribbonDisplay (true/False) |
| 87 | ribbonDrawMode (2D, edged, round, custom) |
| 88 | ribbonColor |
| 89 | ribbonXSection (for custom cross-sections) |
| 90 | ribbonStyle (width and thickness scale factors, e.g. for worms) |
| 91 | |
| 92 | fillDisplay (true/false, fill rings in residue) |
| 93 | fillMode (thin, thick) |
| 94 | fillColor |
| 95 | |
| 96 | label (text) |
| 97 | labelColor |
| 98 | labelOffset (xyz position relative to residue CA?) |
| 99 | |
| 100 | == Nucleotides - nucleic acid slab depictions in Python/VRML in Chimera 1 == |
| 101 | *These attributes should probably be moved to Residue C++ object in Chimera 2 |
| 102 | |
| 103 | style (sugar base styles: fill/slab, fill/fill, tube/slab, ladder, atoms+bonds) |
| 104 | baseOrientationIndicator (true/false) |
| 105 | slabThickness (float) |
| 106 | slabShape (box, tube, ellipsoid) |
| 107 | slabColor |
| 108 | hideBaseAtoms (true/false) |
| 109 | separateGlycosidicBond (true/false) |
| 110 | slabDimensionsPurines (lower left, upper right xy offsets) |
| 111 | slabDimensionsPyrimidines (lower left, upper right xy offsets) |
| 112 | anchor (base, sugar) |
| 113 | slabStyle (long, big, fat, skinny) |
| 114 | ladderIgnoreNonBaseHBonds (true/false) |
| 115 | ladderShowStubs (true/false) |
| 116 | ladderRungRadius (float) |
| 117 | ladderUseExistingHBonds (true/false) |
| 118 | ladderRelaxHBondConstraints (true/false) |
| 119 | ladderHBondConstraints(angstroms and degrees, if relax enabled) |
| 120 | |
| 121 | == Chain == |
| 122 | No graphical attributes, Chain class does not exist in Chimera 1 |
| 123 | |
| 124 | *Might put Pipes and Planks graphical attributes in Chain or Residue. |
| 125 | Current pipes and planks attributes: |
| 126 | |
| 127 | helixColor |
| 128 | helixEdgeColor |
| 129 | showArrowOnHelix (true/false) |
| 130 | fixedHelixRadius (true/false) |
| 131 | helixRadius (float) |
| 132 | splitCurvedHelices(true/false) |
| 133 | helixSplitThreshold (float, where to split) |
| 134 | |
| 135 | strandColor |
| 136 | strandEdgeColor |
| 137 | showArrowOnStrand (true/false) |
| 138 | fixedStrandThickness (true/false) |
| 139 | strandThickness (float) |
| 140 | splitCurvedStrands(true/false) |
| 141 | strandSplitThreshold (float, where to split) |
| 142 | |
| 143 | displayCoil (true/false) |
| 144 | coilColor |
| 145 | coilEdgeColor |
| 146 | coilSubdivision (integer, level of detail) |
| 147 | coilWidth (float) |
| 148 | coilThickness (float) |
| 149 | |
| 150 | == Molecule, also inherits from Model == |
| 151 | ballScale (float, scale ball size in ball and stick) |
| 152 | pointSize (pixels for dot display) |
| 153 | |
| 154 | autoChain (true/false, connect CA atoms with pseudobonds) |
| 155 | stickScale (float, scale factor for bond radius) |
| 156 | lineWidth (pixels, for wire display) |
| 157 | lineType (solid, dash, dot, dash-dot, dash-dot-dot) |
| 158 | wireStipple (stipple pattern for wire bonds) |
| 159 | showStubBonds (true/false, show a bond if atom not shown?) |
| 160 | |
| 161 | ribbonType (bspline, cardinal) |
| 162 | ribbonStiffness (float, interpolation parameter) |
| 163 | ribbonSmoothing (strand | coil mask, to smooth specific secondary structures) |
| 164 | ribbonInsideColor (for inside/outside dual coloring) |
| 165 | ribbonHidesMainChain (true/false) |
| 166 | residueLabelPositionMode (centroid, backbone, primary-atom) |
| 167 | |
| 168 | aromaticDisplay (true/false, show circle or disk in aromatic rings) |
| 169 | aromaticMode (circle, disk) |
| 170 | aromaticLineType (solid, dash, dot, ... for circle display) |
| 171 | |
| 172 | *surfaceColor (drop this, for single color molecular surface, use surface attribute) |
| 173 | *surfaceOpacity (drop this, for molecular surface, use surface attribute) |
| 174 | *vdwDensity (drop this, density of surface vertices) |
| 175 | |
| 176 | == Model == |
| 177 | display (true/false) |
| 178 | |
| 179 | color |
| 180 | |
| 181 | useClipPlane (true/False) |
| 182 | clipPlane (center point and normal) |
| 183 | useClipThickness (true/false, clip to a slab) |
| 184 | clipThickness (float, slab thickness) |
| 185 | |
| 186 | silhouette (true/false, silhouettes enabled for this model) |
| 187 | |
| 188 | == PseudoBondGroup (global bond settings like Molecule) == |
| 189 | stickScale (float, scale factor for bond radius) |
| 190 | lineWidth (pixels, for wire display) |
| 191 | lineType (solid, dash, dot, dash-dot, dash-dot-dot) |
| 192 | wireStipple (stipple pattern for wire bonds) |
| 193 | showStubBonds (true/false, show a bond if atom not shown?) |
| 194 | |
| 195 | == Other changes == |
| 196 | |
| 197 | 1. Make color objects immutable. Chimera 1 allows redefining a color and having all graphics objects |
| 198 | using that color automatically update. Complexity of that is not worth it. |
| 199 | |
| 200 | 2. Integrating Nucleotides, Thermal ellipsoid, and Pipes and Plank styles into core is a lot of work. |