Hi Gianluca,
Unfortunately, Pymol offers no such functionality intrinsically. But
this is where python comes in handy. Attached you find a script I
wrote for the purpose. It allows you to shift objects or selections
over the periodic lattice:
run lattice.py
create ObjectCopy,MyObject
shift 1,0,0,ObjectCopy # make one shift over the first vector of the lattice
shift 0,1,0,ObjectCopy # make one shift over the second vector of the lattice
shift 2,2,2,ObjectCopy # make two shifts over each of the vectors of
the lattice
Hope it helps,
Tsjerk
On 4/19/07, Gianluca Santarossa <gianluca.santaro...@chem.ethz.ch> wrote:
Dear all,
is there a way to show the periodic images from a slab in PyMOL?
Thanks,
Gianluca
--
==============================================================
Gianluca Santarossa
Institute for Chemical and Bioengineering
Department of Chemistry and Applied Biosciences
ETH Zurich, Hönggerberg, HCI, 8093 Zurich
Phone: +41 44 633 4232
E-Mail: gianluca.santaro...@chem.ethz.ch
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
from pymol import cmd
from math import *
def triclinic(L):
B = [[0,0,0],[0,0,0],[0,0,0]]
x, y, z, a, b, c = L[:6]
B[0][0] = x
if a == 90 and b == 90 and c == 90:
B[1][1] = y
B[2][2] = z
else:
a = a*pi/180
b = b*pi/180
c = c*pi/180
B[1][0] = y*cos(c)
B[1][1] = y*sin(c)
B[2][0] = z*cos(b)
B[2][1] = z*(cos(a)-cos(b)*cos(c))/sin(c)
B[2][2] = sqrt(z*z-B[2][0]**2-B[2][1]**2)
return B
def get_lattice(selection=""):
if selection:
S = cmd.get_symmetry(selection)
else:
S = cmd.get_symmetry()
print S
return triclinic(S)
def shift(n1=0,n2=0,n3=0,selection="",L=None):
n1, n2, n3 = float(n1), float(n2), float(n3)
if not L:
L = get_lattice(selection)
if not selection:
selection = "all"
cmd.alter_state(1,selection,"(x,y,z)=(x+%f,y+%f,z+%f)"
%(n1*L[0][0]+n2*L[1][0]+n3*L[2][0],
n1*L[0][1]+n2*L[1][1]+n3*L[2][1],
n1*L[0][2]+n2*L[1][2]+n3*L[2][2]))
cmd.extend("get_lattice",get_lattice)
cmd.extend("shift",shift)
