Re: [PyMOL] drawing a bond between the same Calpha atom in different states
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.cahttp://pldserver1.biochem.queensu.ca/~rlc
--
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post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
Canada
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Re: [PyMOL] drawing a bond between the same Calpha atom in different states
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.ukwrote:
thanks tsjerk
ive been playing with the values at the end..and i can,t change it
to go from
white to blueor even red to blue
i triedwhite to blueso 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 1,1,1where 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,1which
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,
[PyMOL] drawing a bond between the same Calpha atom in different states
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 Many thanks for the help. 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 -- 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
Re: [PyMOL] drawing a bond between the same Calpha atom in different states
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. Hope that helps. 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.cahttp://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
Re: [PyMOL] drawing a bond between the same Calpha atom in different states
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.cahttp://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
