def MethodOne():
Midas.close("all")
openMolecule(pdbid)
efhand = "#0:117-147"
calcium = "#0:151.het"
backboneAtoms = "@n,c,ca,o"
negRes = "::asp,glu"
# Display EF-Hand
Midas.represent("bs", efhand)
Midas.show(efhand + "&" + negRes)
Midas.color("green", efhand + "&" + negRes)
Midas.color("cyan", "#0:135")
Midas.color("byatom", efhand + backboneAtoms)
# Midas.resrepr("edged", efhand)
Midas.resrepr("smooth", "#0")
# Display Calcium
Midas.display(calcium)
Midas.color("cyan", calcium)
Midas.vdwdefine("ca", "ca", 0.5, calcium)
Midas.represent("sphere", calcium)
# Adjust View
Midas.center(calcium)
Midas.cofr(calcium)
chimera.viewer.scaleFactor = 7
# Add Feature Shells
s = FeatureShellNode(6, 1, sphereColor=(.2, 0, .4), sphereTransparency=.1)
t = apply(newTranslation, getLocation(calcium))
t.addChild(s.spheres)
useVRML(t, name="FEATURE Spheres")
t = apply(newTranslation, getLocation(calcium))
t.addChild(s.circles)
useVRML(t, name="FEATURE Rings")
# Add Markers
markerSize = 1
markerColor = "yellow"
alphaLoc = (26.768, 15.445, 3.308)
betaLoc = (24.006, 18.672, 1.650)
centroidLoc = (27.1862, 17.9809, 1.31815)
g = GroupNode()
g.addChild(newMarker(alphaLoc, markerSize, markerColor))
g.addChild(newMarker(betaLoc, markerSize, markerColor))
g.addChild(newMarker(centroidLoc, markerSize, markerColor))
#useVRML(g,name="FEATURE Markers")
# Show Water
water = "#0:231.water"
Midas.display(water)
Midas.vdwdefine("hoh", "o", 0.2, water)
Midas.represent("sphere", water)
def MethodTwo():
Midas.close("all")
# Parameters
featureNumShells = 6
featureShellThickness = 1.0
# Load Molecule
modelSel = "#0"
[mol] = chimera.openModels.open(pdbfilename)
chimera.viewer.scaleFactor = 4.5
# Draw as Ribbon
Midas.resrepr("smooth", modelSel)
for res in mol.residues:
res.drawMode = chimera.Residue.Ribbon_Edged
# Display Calciums
calciumsSel = modelSel + "::ca"
Midas.vdwdefine("ca", "ca", 0.5, calciumsSel)
Midas.show(calciumsSel)
Midas.represent("sphere", calciumsSel)
# Display Shells
calciums = Midas._selectedAtoms(calciumsSel)
featureModels = []
for calcium in calciums:
location = calcium.coord().xyz.data()
t = apply(newTranslation, location)
f = FeatureShellNode(featureNumShells, featureShellThickness)
t.addChild(f)
featureModels += useVRML(t, name="FEATURE Shell")
# Load hitsfile
import viewhitfile
viewhitfile.loadFile(hitfilename)