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:
10                                                                     
      

nrib

None
Value:
2                                                                      
      

nres

None
Value:
46                                                                     
      

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)