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From: Gareth S. <ga...@eb...> - 2003-07-18 10:47:07
|
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 <ga...@eb...> European Bioinformatics Institute |
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From: Gareth S. <ga...@eb...> - 2003-07-21 08:14:39
|
Regarding the h-bond code I posted the other day, (1) The formatting got all screwed up in the e-mail. (Thanks to Cameron Mura for pointing this out) (2) Michael Lerner mailed me an improved version of the code which can automatically number the h-bond objects hbond01, hbond02 etc, if explicit names aren't supplied The new version, with correct indenting, is available for download at http://www.ebi.ac.uk/~gareth/work/pymol Gareth -- Gareth Stockwell <ga...@eb...> European Bioinformatics Institute |
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From: Warren L. D. <wa...@de...> - 2003-07-18 15:35:08
|
Gareth, CGO is currently the way to go... Cheers, Warren -- mailto:wa...@de... Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -----Original Message----- > From: pym...@li... [mailto:pymol-users- > ad...@li...] 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 <ga...@eb...> > European Bioinformatics Institute > > > > ------------------------------------------------------- > This SF.net email is sponsored by: VM Ware > With VMware you can run multiple operating systems on a single machine. > WITHOUT REBOOTING! Mix Linux / Windows / Novell virtual machines at the > same time. Free trial click here: http://www.vmware.com/wl/offer/345/0 > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users |
|
From: Gareth S. <ga...@eb...> - 2003-07-18 16:51:38
|
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:wa...@de...
> Warren L. DeLano, Ph.D.
> Principal Scientist
> DeLano Scientific LLC
> Voice (650)-346-1154
> Fax (650)-593-4020
>
> > -----Original Message-----
> > From: pym...@li... [mailto:pymol-users-
> > ad...@li...] 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 <ga...@eb...>
> > European Bioinformatics Institute
> >
> >
> >
> > -------------------------------------------------------
> > This SF.net email is sponsored by: VM Ware
> > With VMware you can run multiple operating systems on a single
> machine.
> > WITHOUT REBOOTING! Mix Linux / Windows / Novell virtual machines at
> the
> > same time. Free trial click here: http://www.vmware.com/wl/offer/345/0
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: VM Ware
> With VMware you can run multiple operating systems on a single machine.
> WITHOUT REBOOTING! Mix Linux / Windows / Novell virtual machines at the
> same time. Free trial click here: http://www.vmware.com/wl/offer/345/0
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
--
Gareth Stockwell <ga...@eb...>
European Bioinformatics Institute
|
|
From: Warren L. D. <wa...@de...> - 2003-07-18 17:25:32
|
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:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
> -----Original Message-----
> From: Gareth Stockwell [mailto:ga...@eb...]
> 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:wa...@de...
> > Warren L. DeLano, Ph.D.
> > Principal Scientist
> > DeLano Scientific LLC
> > Voice (650)-346-1154
> > Fax (650)-593-4020
> >
> > > -----Original Message-----
> > > From: pym...@li... [mailto:pymol-users-
> > > ad...@li...] 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 <ga...@eb...>
> > > European Bioinformatics Institute
> > >
> > >
> > >
> > > -------------------------------------------------------
> > > This SF.net email is sponsored by: VM Ware
> > > With VMware you can run multiple operating systems on a single
> > machine.
> > > WITHOUT REBOOTING! Mix Linux / Windows / Novell virtual machines
> > > at
> > the
> > > same time. Free trial click here:
> > > http://www.vmware.com/wl/offer/345/0
> > > _______________________________________________
> > > PyMOL-users mailing list
> > > PyM...@li...
> > > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
> >
> >
> > -------------------------------------------------------
> > This SF.net email is sponsored by: VM Ware
> > With VMware you can run multiple operating systems on a single
> > machine. WITHOUT REBOOTING! Mix Linux / Windows / Novell virtual
> > machines at the same time. Free trial click here:
> > http://www.vmware.com/wl/offer/345/0
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> --
> Gareth Stockwell <ga...@eb...>
> European Bioinformatics Institute
|
|
From: Gareth S. <ga...@eb...> - 2003-07-18 18:37:41
|
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:wa...@de...
> Warren L. DeLano, Ph.D.
> Principal Scientist
> DeLano Scientific LLC
> Voice (650)-346-1154
> Fax (650)-593-4020
>
> > -----Original Message-----
> > From: Gareth Stockwell [mailto:ga...@eb...]
> > 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:wa...@de...
> > > Warren L. DeLano, Ph.D.
> > > Principal Scientist
> > > DeLano Scientific LLC
> > > Voice (650)-346-1154
> > > Fax (650)-593-4020
> > >
> > > > -----Original Message-----
> > > > From: pym...@li... [mailto:pymol-users-
>
> > > > ad...@li...] 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 <ga...@eb...>
> > > > European Bioinformatics Institute
> > > >
> > > >
> > > >
> > > > -------------------------------------------------------
> > > > This SF.net email is sponsored by: VM Ware
> > > > With VMware you can run multiple operating systems on a single
> > > machine.
> > > > WITHOUT REBOOTING! Mix Linux / Windows / Novell virtual machines
> > > > at
> > > the
> > > > same time. Free trial click here:
> > > > http://www.vmware.com/wl/offer/345/0
> > > > _______________________________________________
> > > > PyMOL-users mailing list
> > > > PyM...@li...
> > > > https://lists.sourceforge.net/lists/listinfo/pymol-users
> > >
> > >
> > >
> > > -------------------------------------------------------
> > > This SF.net email is sponsored by: VM Ware
> > > With VMware you can run multiple operating systems on a single
> > > machine. WITHOUT REBOOTING! Mix Linux / Windows / Novell virtual
> > > machines at the same time. Free trial click here:
> > > http://www.vmware.com/wl/offer/345/0
> > > _______________________________________________
> > > PyMOL-users mailing list
> > > PyM...@li...
> > > https://lists.sourceforge.net/lists/listinfo/pymol-users
> > --
> > Gareth Stockwell <ga...@eb...>
> > European Bioinformatics Institute
>
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: VM Ware
> With VMware you can run multiple operating systems on a single machine.
> WITHOUT REBOOTING! Mix Linux / Windows / Novell virtual machines at the
> same time. Free trial click here: http://www.vmware.com/wl/offer/345/0
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
--
Gareth Stockwell <ga...@eb...>
European Bioinformatics Institute
|
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