Section RenderWindow
backgroundColor (1.0, 1.0, 1.0) // background color
rotateButtonMask 1 // right button
panButtonMask 2 // middle button
zoomButtonMask 4 // left button
Section SpaceBall4000FLX
devicePort /dev/ttyS0
linearGain 0.0005
angularGain 0.001
zTranslationModeButtonIndex 9
zTranslationModeButtonToggle true
dollyGain 0.02
maxOnlyButtonIndex 10
maxOnlyButtonToggle true
dragButtonIndex 0
dragButtonToggle true
EndSection
EndSection
Section RamachandranPlot
backgroundColor (0.0, 0.0, 0.0) // background color
selectedStructureColor (1.0, 1.0, 1.0) // color in RGB for dihedral angles of the selected secondary structure
activeCoilRegionColor (0.0, 0.0, 0.0) // color in RGB for dihedral angles of all active coil regions
EndSection
Section ProteinRenderer
Section AlphaHelix // default setting values of per AlphaHelix structure
drawAtoms true
drawBonds true
drawCPK true
drawTube true
drawLine true
bondWidth 2.0
bondColor (1.0, 0.0, 0.0) // color in RGB
drawBackbone true
backboneWidth 4.0
drawBackboneRibbon true
backboneRibbonWidth 2.0
drawCartoon true
backboneColor
drawHydrogenBondSites false
hydrogenBondSiteDiameter 5.0
hydrogenBondSiteWidth 1.0
amideColor (0.5, 0.5, 1.0) // color in RGB
carboxylColor (1.0, 0.0, 0.0) // color in RGB
drawHydrogenCages false
hydrogenCageWidth 1.5
hydrogenCageColor (0.6, 0.5, 0.0) // color in RGB
hydrogenCageLarge false
EndSection
Section BetaStrand // default setting values of per BetaStrand structure
drawAtoms true
drawBonds true
drawCPK true
drawTube true
drawLine true
bondWidth 2.0
bondColor (1.0, 0.0, 0.0) // color in RGB
drawBackbone true
backboneWidth 4.0
drawBackboneRibbon true
backboneRibbonWidth 2.0
drawCartoon true
backboneColor
drawHydrogenBondSites true
hydrogenBondSiteDiameter 5.0
hydrogenBondSiteWidth 1.0
amideColor (0.5, 0.5, 1.0) // color in RGB
carboxylColor (1.0, 0.0, 0.0) // color in RGB
drawHydrogenCages true
hydrogenCageWidth 1.5
hydrogenCageColor (0.6, 0.5, 0.0) // color in RGB
hydrogenCageLarge true
EndSection
Section Coil // default setting values of per coil structure
drawAtoms true
drawBonds true
drawCPK true
drawTube true
drawLine true
bondWidth 2.0
bondColor (1.0, 0.0, 0.0) // color in RGB
drawBackbone true
backboneWidth 4.0
drawBackboneRibbon true
backboneRibbonWidth 2.0
drawCartoon true
backboneColor
drawHydrogenBondSites false
hydrogenBondSiteDiameter 5.0
hydrogenBondSiteWidth 1.0
amideColor (0.5, 0.5, 1.0) // color in RGB
carboxylColor (1.0, 0.0, 0.0) // color in RGB
drawHydrogenCages false
hydrogenCageWidth 1.5
hydrogenCageColor (0.6, 0.5, 0.0) // color in RGB
hydrogenCageLarge false
EndSection
drawAtoms false // global default setting values
atomMaterial (0.1, 0.1, 0.1), (1.0, 1.0, 1.0), (1.0, 1.0, 1.0), 25.0 // in ambient,diffuse,specular,shininess format
atomTesselation 4
drawBonds false
bondMaterial (0.1, 0.1, 0.1), (1.0, 0.0, 0.0), (1.0, 1.0, 1.0), 25.0 // in ambient,diffuse,specular,shininess format
numBondVertices 24
bondRadius 0.25
numLineVertices 6
lineRadius 0.15
cpkSphereRadius 0.3
drawCPK false
drawTube false
drawLine false
alphaHelixColor (1.0, 0.0, 0.7) // color in RGB
betaStrandColor (0.7, 0.0, 1.0) // color in RGB
coilColor (1.0, 0.0, 1.0) // color in RGB
hydrophobicColor (1.0,1.0,1.0) // color in RGB
hydrophilicColor (0.5,0.5,1.0) // color in RGB
disulfideColor (0.75,0.5,0.0) // color in RGB
highlightColor (1.0, 1.0, 0.0) // color in RGB
drawBackbone false
drawBackboneRibbon false
backboneRibbonMaterial (0.05, 0.05, 0.05), (1.0, 0.0, 1.0), (1.0, 1.0, 1.0), 50.0 // in ambient,diffuse,specular,shininess format
backboneRibbonUseAllAtoms false
backboneRibbonDegree 3
backboneRibbonSampleDensity 16
drawCartoon true
cartoonMaterial (0.05, 0.05, 0.05), (1.0, 0.0, 1.0), (1.0, 1.0, 1.0), 50.0 // in ambient,diffuse,specular,shininess format
cartoonDegree 3
cartoonSampleDensity 16
alphaHelixWidth 1.5
alphaHelixThickness 0.5
betaStrandWidth 1.5
betaStrandThickness 0.5
betaStrandHeadWidth 1.5
numCoilVertices 8
coilRadius 0.333
drawHydrogenBonds true
hydrogenBondWidth 3.0
hydrogenBondColor (0.7, 0.6, 0.0) // color in RGB
drawHydrogenBondSites false
drawHydrogenCages false
drawCollisions false
collisionSphereMaterial (0.1, 0.1, 0.1), (1.0, 0.0, 0.0), (1.0, 1.0, 1.0), 25.0 // in ambient,diffuse,specular,shininess format
collisionSphereTesselation 4
grayOutCartoon false // toggle the color change of the second protein when doing alignment
grayOutColor (0.9, 0.9, 1.0) // color in RGB for the second protein when doing alignment
EndSection
Section BuildBeta
interact 1 // 1: the program stops after every structure, or 2: multiple time per structure, and queries the user whether to enter interactive mode.
optimized_angles 0 // 0: the beta strands are flattened using standard phi and psi angles, or 1: optimized angles depending on the amino acid position, strand length, and up directions of adjacent strands are used
flatten 1 // 1: flatten the beta strands
flatfrac .7 // the fraction of the way between the nominal beta strand phi and psi angles in the middle of the distribution on the Ramachandran plot, and the completely flattened values for no twist in the strand
strand_to_coil_penalty 1. // the energy estimate is increased by the beta strand prediction certainty times strand_to_coil_penalty when the predicted strands is shortened
offlineBuildBeta 0 // 1: create the conformation files without any display or user input
spacing 18. // the distance between the beta sheet and any alpha helices, and also between the layers of alpha helices
shorten 1 // 1: the predicted strands will be shortened to account for the limits of matching with any adjacent strands
move_helices 0 // 1: Build Beta makes an attempt to move at least the alpha helices away from the beta sheet
try_topologies 6 // the number of topologies considered
enough_topologies 4 // the max number for topology success count before BuildBeta returns
EndSection
Section ProteinCreator
addHydrogens true // add a missing hydrogen atom (amide proton) for the second and subsequent residues
fabricatedAtomDistance 1.1 // a distance for fabricating a new atom for the missing hydrogen
chainSelection A B // selection of chain ID(s)
multipleModel 1 2 // selection of model ID(s)
EndSection
Section EnergyCalculator
addCaps true // cap ACE and NME at the ends of amino acid sequence to make the protein ready for the energy calculation
conTol 1.49012e-08 // constraint tolerance for LBFGS local optimization
fcnTol 1e-12 // function tolerance for LBFGS local optimization
gradTol 6.05545e-06 // gradient tolerance for LBFGS local optimization
lineSearchTol 0.0001 // lineseach tolerance for LBFGS local optimization
maxStep 1e+20 // maximum step for LBFGS local optimization
maxIter 100000 // maximum number of iterations for LBFGS local optimization
maxBacktrackIter 5 // maximum number of backtrack iterations for LBFGS local optimization
maxFeval 1000 // maximum number of function evaluations for LBFGS local optimization
minStep 1e-20 // minimum required step for LBFGS local optimization
stepTol 1e-9 // step tolerance for LBFGS local optimization
verboseThreadTrace true // if true, log verbose output from the local optimization thread
maxBuffer 4096 // maximum size of volume visualization buffer in megabytes
autoSaveGLState true // if true, automatically set and clear OpenGL attributes for volume rendering
sliceFactor 0.707 // slicing distance for 3D texture rendering (not used for 2D textures)
textureCaching true // if true, use OpenGL texture caching
updateInterval 20 // number of LBFGS iterations to run for each visual update
interpolationMode 1 // for textures, 0 = constant interpolation, 1 = linear interpolation (OpenGL parameter)
renderingMode 1 // for textures, 0 = 2D textures, 1 = 3D textures (may be overridden if OpenGL does not support sufficiently large 3D textures)
textureFunction 0 // for textures, 0 = replace, 1 = modulate (OpenGL parameter)
voxelAlignment 1 // for textures, 0 = vertex centered, 1 = cell centered
recordFileName minimization.record // name of the record file created when the "record" toggle is selected
enginePath lib // the path to the energy library
dsoName lib/libAmber.so // the name of the energy library
EndSection