ProteinShop.cfg

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