Hey :)
Can't resist the challenge...
For any given ensemble, you can draw a trace through the C-alphas using the
following lines, illustrated here for the NMR ensemble '1NMR':
# Get the structure
fetch 1nmr
# Get the number of states
n = cmd.count_states('1nmr')
# Collect the C-alpha coordinates
# This calls get_model for every state and extracts the coordinates for
every model-state
# The resulting list is transposed, such that each list entry contains the
coordinates for one C-alpha over all states
x=zip(*[cmd.get_model('1nmr and n. ca',state=i+1).get_coord_list() for i in
range(n)] )
# Now draw the traces by building a CGO model
cmd.load_cgo([i for j in x for u,v,f in zip(j,j[1:],range(r)) for i in
[9.0]+u+v+[0.1,1,1-(1.*f)/r,1-(1.*f)/r,1,1-(1.+f)/r,1-(1.+f)/r]],"trace")
The 9.0 is the CGO code for a cylinder (pymol.cgo.CYLINDER). The 0.1 is the
radius, and the following six values are the start and end RGB values,
which are related to the state number, such that they end up from white to
red. For more complex colors it would be nice to have a rgb() function that
would return a color according to some scheme, given a fraction, which
would make that last command
cmd.load_cgo([i for j in x for u,v,f in zip(j,j[1:],range(r)) for i in
[9.0]+u+v+[0.1]+rgb((1.*f)/r,scheme=...)+rgb((1.+f)/r,scheme=...)],"trace")
Hope it helps,
Tsjerk
On Thu, Dec 13, 2012 at 10:54 PM, Robert Campbell <
robert.campb...@queensu.ca> wrote:
> Hi,
>
> (replying to my own message)
>
> On Thu, 2012-12-13 15:52 EST, Robert Campbell
> <robert.campb...@queensu.ca> wrote:
>
> > Hi Jon,
> >
> > On Thu, 2012-12-13 16:09 EST, Jonathan Grimes <
> jonat...@strubi.ox.ac.uk>
> > wrote:
> >
> > > Hi All,
> > >
> > > I have 2 different states of the same molecule......different
> > > conformations generated from MD, so the same number of Calpha atoms,
> > > with a direct 1:1 mapping between Calphas with the same residue
> > > numbering.
> > >
> > > I would like to draw a "bond" between equivalent C-alpha atoms, and
> I
> > > will then ramp colour along the bond, say blue-white-red.
> > >
> > > Could I get advice how to draw a bond between 2 Calpha atoms (same
> > > resi) from different states
> >
> > I have a script for drawing a cylinder (you can specify the radius and
> the
> > beginning and ending colors) between two atoms. The script is at:
> >
> >
> http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/draw_cylinder_cgo.py
> >
> > First "run" the script via the "File" menu or via the command line:
> >
> > run draw_cylinder_cgo.py
> >
> > You will then have two new functions defined "draw_cylinder" and
> > "draw_cylinder_cgo". The former allows you to pick two atoms to draw the
> > cylinder between:
> >
> > draw_cylinder name, atom1, atom2, radius, start_color, end_color
> >
> > where each atom is a standard PyMOL selection (defaults to pk1 and
> > pk2) and color is a 3-element RGB tuple defining the color
> > of the cylinder (where each value of R, G and B is between 0 and 1
> > inclusive). The colors default to (1,1,0).
> >
> >
> > Alternatively, draw_cylinder_cgo takes as arguments the start and end
> > coordinates of the vector in place of atom1 and atom2.
>
> I could add more instructions here. You can specify the colours by
> name and if you have picked the atoms with the mouse you can easily do
> something like:
>
> draw_cylinder dist1, start_color=red, end_color=yellow
>
> and it will default to using atom selections "pk1" and "pk2" and a radius
> of 0.1 A.
>
> Cheers,
> Rob
> --
> Robert L. Campbell, Ph.D.
> Senior Research Associate/Adjunct Assistant Professor
> Dept. of Biomedical & Molecular Sciences
> Botterell Hall Rm 644
> Queen's University,
> Kingston, ON K7L 3N6 Canada
> Tel: 613-533-6821
> <robert.campb...@queensu.ca> http://pldserver1.biochem.queensu.ca/~rlc
>
>
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--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
Canada
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