Hi Jon,
You also have to update the three numbers before. So to go from white to
blue is
cmd.load_cgo([i for j in x for u,v,f in zip(j,j[1:],range(n)) for i in
[9.0]+u+v+[1.3, 1-(1.*f)/n,1-(1.*f)/n,1, 1-(1.+f)/n,1-(1.+f)/n,1
]],"trace")
If you want to go from blue to white to red, it's probably easiest to split
it in two:
a=n/2
b=n-n/2
cmd.load_cgo([i for j in x for u,v,f in zip(j,j[1:],range(n))[:a] for i in
[9.0]+u+v+[1.3, (1.*f)/a,(1.*f)/a,1, (1.+f)/a,(1.+f)/a,1 ]],"trace_a")
cmd.load_cgo([i for j in x for u,v,f in zip(j,j[1:],range(n))[a:] for i in
[9.0]+u+v+[1.3, 1,1-(1.*f-a)/b,1-(1.*f-a)/b,
1,1-(1.+f-a)/b,1-(1.+f-a)/b ]],"trace_b")
For the capping, you can use spheres:
cmd.load_cgo([i for j in x for u,f in zip(j,range(n))[:a] for i in [6.0,
(1.*f)/a,(1.*f)/a,1, 7.0]+u+[1.3]],"spheres_a")
cmd.load_cgo([i for j in x for u,f in zip(j,range(n))[a:] for i in [6.0,
1,1-(1.*f-a)/b,1-(1.*f-a)/b, 7.0]+u+[1.3]],"spheres_b")
For more complex color schemes, you would definitely want a rgb function.
Hope it helps,
Tsjerk
On Fri, Dec 14, 2012 at 12:25 PM, Jonathan Grimes
<jonat...@strubi.ox.ac.uk>wrote:
>
> thanks tsjerk
>
> ive been playing with the values at the end......and i can,t change it
> to go from
> white to blue....or even red to blue....
>
> i tried....white to blue....so 1,1,1 to 0,0, 1
>
> cmd.load_cgo([i for j in x for u,v,f in zip(j,j[1:],range(n)) for i in
> [9.0]+u+v+[1.3,1,1-(1.*f)/n,1-(1.*f)/n, 1-(1.+f)/n,1-(1.+f)/n,1 ]],"trace")
>
> so 1,1-(1.*f)/n,1-(1.*f)/n, corresponds to 1,1,1....where f/n is the
> fraction along the cylinder.....
>
> and then i changed the last 3 numbers to 1-(1.+f)/n,1-(1.+f)/n,1....which
> i thought would go to 0 , 0 ,1
>
> but i get a bond but the color doesnt go smoothly from white to blue ??
>
> is there also a nice way to cap the cylinder so it had a rounded end ??
>
> thanks
> jon
>
>
> Dr. Jonathan M. Grimes,
> NDM Senior Reseach Fellow
> University Research Lecturer
> Division of Structural Biology
> Wellcome Trust Centre for Human Genetics
> University of Oxford
> Roosevelt Drive,
> Oxford OX3 7BN, UK
>
> Email: jonat...@strubi.ox.ac.uk, Web: www.strubi.ox.ac.uk
> Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547
>
>
>
> On 14 Dec 2012, at 09:13, Tsjerk Wassenaar wrote:
>
> 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
>>
>>
>> ------------------------------------------------------------------------------
>> LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
>> Remotely access PCs and mobile devices and provide instant support
>> Improve your efficiency, and focus on delivering more value-add services
>> Discover what IT Professionals Know. Rescue delivers
>> http://p.sf.net/sfu/logmein_12329d2d
>> _______________________________________________
>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Biocomputing Group
> Department of Biological Sciences
> 2500 University Drive NW
> Calgary, AB T2N 1N4
> Canada
>
> ------------------------------------------------------------------------------
> LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
> Remotely access PCs and mobile devices and provide instant support
> Improve your efficiency, and focus on delivering more value-add services
> Discover what IT Professionals Know. Rescue delivers
>
> http://p.sf.net/sfu/logmein_12329d2d_______________________________________________
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
>
>
--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
Canada
------------------------------------------------------------------------------
LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
Remotely access PCs and mobile devices and provide instant support
Improve your efficiency, and focus on delivering more value-add services
Discover what IT Professionals Know. Rescue delivers
http://p.sf.net/sfu/logmein_12329d2d
_______________________________________________
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
