Hi Nick,
I recently was playing with (aka learning) the crystallographic symmetry
information in PDB files and now took your feature request as an
exercise. See attached file, hope it does what you had in mind.
Cheers,
Thomas
On Mon, 2010-04-12 at 14:12 -0600, Nicolas Bock wrote:
> It would be great if pymol had support for constructing and displaying
> a supercell:
>
> For data files that support crystallographic information, e.g. pdb,
> pymol can already display the unit cell (show cell). It would be great
> if one could easily display multiple copies of the unit cell, along
> the lines of
>
> supercell 1,1,2
>
> where pymol would then copy the unit cell along the c-axis and display
> 2 unit cells.
>
> supercell 2,2,2
>
> would display 2 copies along the a, b, and c axes, and display 8 unit
> cells in total.
>
> As a related request it would be great if pymol could construct a unit
> cell in case the crystallographic information in the input file does
> not exist. This could come in handy for instance when reading from
> xyz. Maybe a command such as
>
> construct_supercell a=10.2, b=10.2, c=15, alpha=90.0, beta=90,
> gamma=90
>
> would construct a cubic cell with dimensions axbxc.
>
> Thanks,
>
> nick
'''
(c) 2010 Thomas Holder
PyMOL python script (load with `run supercell.py`)
Usage: See "help supercell"
'''
from pymol import cmd, cgo
from math import cos, sin, radians, sqrt
import numpy
def cellbasis(angles, edges):
'''
For the unit cell with given angles and edge lengths calculate the basis
transformation (vectors) as a 4x4 numpy.array
'''
rad = [radians(i) for i in angles]
basis = numpy.identity(4)
basis[0][1] = cos(rad[2])
basis[1][1] = sin(rad[2])
basis[0][2] = cos(rad[1])
basis[1][2] = (cos(rad[0]) - basis[0][1]*basis[0][2])/basis[1][1]
basis[2][2] = sqrt(1 - basis[0][2]**2 - basis[1][2]**2)
edges.append(1.0)
return basis * edges # numpy.array multiplication!
def supercell(a=1, b=1, c=1, object=None, color='blue'):
'''
DESCRIPTION
Draw a supercell, as requested by Nicolas Bock on the pymol-users
mailing list (Subject: [PyMOL] feature request: supercell construction
Date: 04/12/2010 10:12:17 PM (Mon, 12 Apr 2010 14:12:17 -0600))
USAGE
supercell a, b, c [, object [, color]]
ARGUMENTS
a, b, c = integer: repeat cell in x,y,z direction a,b,c times
{default: 1,1,1}
object = string: name of object to take cell definition from
color = string: color of cell {default: blue}
SEE ALSO
show cell
'''
if object is None:
object = cmd.get_object_list()[0]
sym = cmd.get_symmetry(object)
cell_edges = sym[0:3]
cell_angles = sym[3:6]
basis = cellbasis(cell_angles, cell_edges)
assert isinstance(basis, numpy.ndarray)
ts = list()
for i in range(int(a)):
for j in range(int(b)):
for k in range(int(c)):
ts.append([i,j,k])
obj = [
cgo.BEGIN,
cgo.LINES,
cgo.COLOR,
]
obj.extend(cmd.get_color_tuple(color))
for t in ts:
shift = basis[0:3,0:3] * t
shift = shift[:,0] + shift[:,1] + shift[:,2]
for i in range(3):
vi = basis[0:3,i]
vj = [
numpy.array([0.,0.,0.]),
basis[0:3,(i+1)%3],
basis[0:3,(i+2)%3],
basis[0:3,(i+1)%3] + basis[0:3,(i+2)%3]
]
for j in range(4):
obj.append(cgo.VERTEX)
obj.extend((shift + vj[j]).tolist())
obj.append(cgo.VERTEX)
obj.extend((shift + vj[j] + vi).tolist())
cmd.load_cgo(obj, 'supercell')
cmd.extend('supercell', supercell)
------------------------------------------------------------------------------
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