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scene.RemoveAll()
#-------------------------------------------------------------------------------
# Loading structure and alignment
#-------------------------------------------------------------------------------
m=io.LoadPDB('data/sh2.pdb')
mp=m.Select('ligand=false')
aln=io.LoadAlignment('data/sh2.aln')
aln.AttachView(0, mp)
aln.SetSequenceOffset(0, 1)
#-------------------------------------------------------------------------------
# Calculate conservation of alignment
# First we set all properties to zero, then let alg.Conservation assign the
# conservation scores to the residues
#-------------------------------------------------------------------------------
seq.alg.Conservation(aln)
#-------------------------------------------------------------------------------
# Setup Graphical Objects for Rendering
#-------------------------------------------------------------------------------
g=gfx.Entity('SH2', m)
s=io.LoadSurface('data/sh2.vert')
gs=gfx.Surface('SH2-surf', s)
scene.Add(gs)
scene.Add(g)
scene.CenterOn(g)
s.Attach(mp.Select('ligand=false'), 8.0)
gr=gfx.Gradient()
gr.SetColorAt(0.0, gfx.Color(0.1, 0.1, 0.8))
gr.SetColorAt(1.0, gfx.Color(0.8, 0.1, 0.1))
gs.ColorBy('cons', gr, 0.8, 1.0,
mol.Prop.Level.RESIDUE)
g.SetRenderMode(gfx.HSC,
m.Select('ligand=false'))
g.SetRenderMode(gfx.CUSTOM,
m.Select('ligand=true'))
g.SetColor(gfx.YELLOW, 'ligand=true')
#-------------------------------------------------------------------------------
# Create alignment viewer and show it on the screen
#-------------------------------------------------------------------------------
seq_viewer=gui.SequenceViewer()
seq_viewer.AddAlignment(aln)
seq_viewer.Show()
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