Changes between Initial Version and Version 1 of MolGraphics


Ignore:
Timestamp:
Jan 6, 2015, 6:10:58 PM (11 years ago)
Author:
Tom Goddard
Comment:

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  • MolGraphics

    v1 v1  
     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
     1971. Make color objects immutable.  Chimera 1 allows redefining a color and having all graphics objects
     198using that color automatically update.  Complexity of that is not worth it.
     199
     2002. Integrating Nucleotides, Thermal ellipsoid, and Pipes and Plank styles into core is a lot of work.