Package Pmv :: Module Ribbon

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Module Ribbon

source code

Functions

[hide private]

cross(b, c)

normalize(v)

bspline(v1, v2, v3, t)

interpPoints(ctrl, nchord)

ribdrw(ctrl, nrib, nchord)

ribbon2D(nrib, ribwid, nchords, offset, natoms, coords, isHelix, off_c=0.5)
Generate ctrl points for protein ribbon, based on ideas on Carson & Bugg, J.Molec.Graphics 4,121-122 (1986)

Variables

[hide private]

cao = Numeric.array(((16.966999, 12.784000, 4.338000), (15...

nchords = 10

nrib = 2

nres = 46

natoms = 2* nres

offset = 1.2

width = 1.5

vi = Viewer()

n = smooth.shape [1]

f = map(lambda x:(x, x+ 1, x+ n+ 1, x+ n), range(smooth....

v = Numeric.array(Numeric.reshape(smooth, (-1, 4)) [:,: 3])

s = Spheres('sph', vertices= v, quality= 5, protected= T...

mol = Read('../1crn.pdb')

allatoms = mol.chains.residues.atoms

caat = allatoms.get('CA')

coords = caat.coords

p = Spheres('CA', centers= coords, radii= 0.6, protected...

Function Details

[hide private]

cross(b, c)

source code

None

normalize(v)

source code

None

bspline(v1, v2, v3, t)

source code

None

interpPoints(ctrl, nchord)

source code

None

ribdrw(ctrl, nrib, nchord)

source code

None

ribbon2D(nrib, ribwid, nchords, offset, natoms, coords, isHelix, off_c=0.5)

source code

Generate ctrl points for protein ribbon, based on ideas on Carson & Bugg, J.Molec.Graphics 4,121-122 (1986)

Ctrl points for Bspline are generated along a line passing through each CA and along the average of the two peptide planes

nrib number of strands in ribbon ribwid total ribbon width nchord number of chords/residue offset amount to offset ctrl points away from CA positions natom number of atoms stored in arrays coords coordinates of CA and O atoms of all residues in strand isHelix set to 1 for residues in alpha helices off_c this parameter has been added to account for DNA/RNA in the coil

Variables Details

[hide private]

cao

None

Value:

Numeric.array(((16.966999, 12.784000, 4.338000), (15.268000, 13.825000
, 5.594000), (13.856000, 11.469000, 6.066000), (14.993000, 9.862000, 7
.443000), (13.660000, 10.707000, 9.787000), (11.393000, 11.308000, 10.
185000), (10.646000, 8.991000, 11.408000), (11.659000, 8.296000, 13.49
1000), (9.448000, 9.034000, 15.012000), (9.490000, 7.519000, 16.819000
), (8.673000, 5.314000, 15.279000), (8.726000, 4.858000, 12.923000), (
8.912000, 2.083000, 13.258000), (7.670000, 2.031000, 11.245000), (5.14
5000, 2.209000, 12.453000), (4.664000, 3.268000, 10.343000), (5.598000
...

nchords

None

Value:

nrib

None

Value:

nres

None

Value:

natoms

None

Value:

2* nres

offset

None

Value:

1.2

width

None

Value:

1.5

vi

None

Value:

Viewer()

n

None

Value:

smooth.shape [1]

f

None

Value:

map(lambda x:(x, x+ 1, x+ n+ 1, x+ n), range(smooth.shape [1]-1))

v

None

Value:

Numeric.array(Numeric.reshape(smooth, (-1, 4)) [:,: 3])

s

None

Value:

Spheres('sph', vertices= v, quality= 5, protected= True)

mol

None

Value:

Read('../1crn.pdb')

allatoms

None

Value:

mol.chains.residues.atoms

caat

None

Value:

allatoms.get('CA')

coords

None

Value:

caat.coords

p

None

Value:

Spheres('CA', centers= coords, radii= 0.6, protected= True)