Warren,
Great - that's what I needed. For those who are interested, I've
attached code below which draws a dashed line between two atoms, with an
arrow on it. It's called with pretty much the same syntax as the
'distance' command.
Gareth
#------------------------------------------------------------------------
from pymol.cgo import *
from pymol import cmd
from math import *
#-------------------------------------------------
# Draw a hydrogen bond
#---------------------------------
def hbond(name,s1,s2,r=1.0,g=1.0,b=0.2):
'''
DESCRIPTION
"hbond" creates a dashed line between two selections, marked with an
arrow.
USAGE
distance name, (selection1), (selection1) , [, r, [, g, [, b] ] ]
name = name of distance object
selection1,selection2 = atom selections
r, g, b = colour
'''
# Convert arguments into floating point values
rr = float(r)
gg = float(g)
bb = float(b)
# Get dash length, gap length and dash radius from PyMOL
# settings
dl = float(cmd.get_setting_tuple("dash_length")[1][0])
gl = float(cmd.get_setting_tuple("dash_gap")[1][0])
dr = float(cmd.get_setting_tuple("dash_radius")[1][0])
# Get tuple containing object and index of atoms in these
# selections
x1 = cmd.index(s1,1)
x2 = cmd.index(s2,1)
# Get number of atoms in each selection
n1 = len(x1)
n2 = len(x2)
if(n1 < 1):
print "Error: selection " + s1 + " has no atoms"
return
if(n2 < 1):
print "Error: selection " + s2 + " has no atoms"
return
# Get objects and atom indices
o1 = x1[0][0]
i1 = x1[0][1]
o2 = x2[0][0]
i2 = x2[0][1]
# Get ChemPy models
m1 = cmd.get_model(o1)
m2 = cmd.get_model(o2)
# Get atoms
a1 = m1.atom[i1-1]
a2 = m2.atom[i2-1]
# Get coords
x1 = a1.coord[0]
y1 = a1.coord[1]
z1 = a1.coord[2]
x2 = a2.coord[0]
y2 = a2.coord[1]
z2 = a2.coord[2]
# Make some nice strings for user feedback
s1 = o1 + "/" + a1.chain + "/" + a1.resn + "." + a1.resi + "/"
+ a1.name
print s1 + "(" + str(x1) + "," + str(y1) + "," + str(z1) + ")"
s2 = o2 + "/" + a2.chain + "/" + a2.resn + "." + a2.resi + "/"
+ a2.name
print s2 + "(" + str(x2) + "," + str(y2) + "," + str(z2) + ")"
# Calculate distances
dx = x2 - x1
dy = y2 - y1
dz = z2 - z1
d = math.sqrt((dx*dx) + (dy*dy) + (dz*dz))
print "distance = " + str(d) + "A"
# Work out how many times (dash_len + gap_len) fits into d
dash_tot = dl + gl
n_dash = math.floor(d / dash_tot)
# Work out step lengths
dx1 = (dl / dash_tot) * (dx / n_dash)
dy1 = (dl / dash_tot) * (dy / n_dash)
dz1 = (dl / dash_tot) * (dz / n_dash)
dx2 = (dx / n_dash)
dy2 = (dy / n_dash)
dz2 = (dz / n_dash)
# Empty CGO object
obj = []
# Generate dashes
x = x1
y = y1
z = z1
for i in range(n_dash):
# Generate a dash cylinder
obj.extend( [ CYLINDER, x, y, z, x+dx1, y+dy1, z+dz1,
dr, rr, gg, bb, rr, gg, bb ] )
# Move to start of next dash
x = x + dx2
y = y + dy2
z = z + dz2
# Add an arrow half way along
# Calculate midpoint
xm = (x1 + x2) / 2
ym = (y1 + y2) / 2
zm = (z1 + z2) / 2
# Vector pointing along the bond
xv = (3.5 * dr / d) * dx
yv = (3.5 * dr / d) * dy
zv = (3.5 * dr / d) * dz
# Rotate step vector 90deg around X axis
xxv = xv
yyv = -1 * zv
zzv = yv
# Add lines
obj.extend( [ CYLINDER, xm-xv-xxv, ym-yv-yyv, zm-zv-zzv,
xm+xv, ym+yv, zm+zv, dr, rr, gg, bb, rr, gg, bb ] )
obj.extend( [ CYLINDER, xm-xv+xxv, ym-yv+yyv, zm-zv+zzv,
xm+xv, ym+yv, zm+zv, dr, rr, gg, bb, rr, gg, bb ] )
# Load the object into PyMOL
cmd.load_cgo(obj, name)
# Add to PyMOL API
cmd.extend("hbond",hbond)
#------------------------------------------------------------------------
On Fri, 2003-07-18 at 18:25, Warren L. DeLano wrote:
> Gareth,
>
> cmd.identify returns the input indexing, which will correspond
> to the PDB file.
>
> cmd.index returns the internal indexing, which will correspond
> to cmd.get_model
>
> help identify
> help index
>
> Cheers,
> Warren
>
>
> --
> mailto:war...@delanoscientific.com
> Warren L. DeLano, Ph.D.
> Principal Scientist
> DeLano Scientific LLC
> Voice (650)-346-1154
> Fax (650)-593-4020
>
> > -----Original Message-----
> > From: Gareth Stockwell [mailto:gar...@ebi.ac.uk]
> > Sent: Friday, July 18, 2003 8:50 AM
> > To: Warren L. DeLano
> > Cc: 'pymol-users'
> > Subject: RE: [PyMOL] H-bond display
> >
> > Warren,
> >
> > I started having a look at this, but I am getting stuck with atom
> > indices. If I make two selections, (lb) and (rb), by clicking on
> > atoms in an object called 'x', then I can get the indices and objects
> > of those atoms by doing
> >
> > x1 = cmd.identify("lb",1)
> > x2 = cmd.identify("rb",1)
> >
> > In my example, printing out x1 and x2 gives the following: [('x', 2)]
> > [('x', 16)]
> >
> > As I clicked on these atoms, the GUI told me that they were,
> > respectively:
> > VAL: /x/1ATP/E/15/CA
> > LYS: /x/1ATP/E/16/NZ
> >
> > But now, if I dump out the contents of the model.atom array, using
> > this
> > code:
> >
> > m = cmd.get_model("x")
> > i = 1
> > for a in m.atom:
> > print str(i) + " -> " + a.chain + "/" + a.resn + "." \
> > + a.resi + "/" + a.name
> > i = i+1
> >
> > Then I see the following
> > 1 -> E/VAL.15/N
> > 2 -> E/VAL.15/CA
> > 3 -> E/VAL.15/CB
> > 4 -> E/VAL.15/CG1
> > 5 -> E/VAL.15/CG2
> > 6 -> E/VAL.15/C
> > 7 -> E/VAL.15/O
> > 8 -> E/LYS.16/N
> > 9 -> E/LYS.16/CA
> > 10 -> E/LYS.16/CB
> > 11 -> E/LYS.16/CG
> > 12 -> E/LYS.16/CD
> > 13 -> E/LYS.16/CE
> > 14 -> E/LYS.16/NZ
> > 15 -> E/LYS.16/C
> > 16 -> E/LYS.16/O
> > 17 -> E/GLU.17/N
> > 18 -> E/GLU.17/CA
> > 19 -> E/GLU.17/C
> > 20 -> E/GLU.17/O
> >
> > So atom number 2 is correct (VAL.15/CA), but in this array, atom 16 is
>
> > the O, not NZ in LYS.16. I presume that ChemPy is re-ordering the
> > atoms some time during the get_model call - how do I resolve this?
> >
> > Gareth
> >
> >
> > On Fri, 2003-07-18 at 16:36, Warren L. DeLano wrote:
> > > Gareth,
> > >
> > > CGO is currently the way to go...
> > >
> > > Cheers,
> > > Warren
> > >
> > >
> > > --
> > > mailto:war...@delanoscientific.com
> > > Warren L. DeLano, Ph.D.
> > > Principal Scientist
> > > DeLano Scientific LLC
> > > Voice (650)-346-1154
> > > Fax (650)-593-4020
> > >
> > > > -----Original Message-----
> > > > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
>
> > > > ad...@lists.sourceforge.net] On Behalf Of Gareth Stockwell
> > > > Sent: Friday, July 18, 2003 2:46 AM
> > > > To: pymol-users
> > > > Subject: [PyMOL] H-bond display
> > > >
> > > >
> > > > I am using distance objects at the moment, to display h-bonding
> > > > contacts. My question is ... is there any easy way to display the
>
> > > > direction of an h-bond using distances (i.e. putting a little
> > > > arrow on the dashed line)?
> > > >
> > > > I am prepared to bash out some functions which do this using CGOs,
>
> > > > but of course I won't if it's already implemented!
> > > >
> > > > Gareth
> > > >
> > > >
> > > > --
> > > > Gareth Stockwell <gar...@ebi.ac.uk>
> > > > European Bioinformatics Institute
> > > >
> > > >
> > > >
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> > >
> > >
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> > --
> > Gareth Stockwell <gar...@ebi.ac.uk>
> > European Bioinformatics Institute
>
>
>
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--
Gareth Stockwell <gar...@ebi.ac.uk>
European Bioinformatics Institute
