From: Jason Vertrees <jason.vertrees@sc...> - 2010-05-12 14:42:43
If you knew the positions of the end points of the lines you could
make CGO lines, or you could just use a distance measure between two
pseudoatoms and modify some label/dash settings:
# make two new pseudoatoms, just for
# making a distance measure between them
# Specify your own position vectors in pos=[x, y, z]
pseudoatom aa, pos=[10.0, -14.0, 33.0]
pseudoatom bb, pos=[-15.3, 44.5, 8.3]
# create distance between the two atoms
distance d1, /aa/////1, /bb/////1
# clean up the representation to make this look
# morel like a solid line
set dash_gap, 0
set dash_radius, 0.55
set dash_round_ends, 0
set dash_color, 0xffcc00, d1
hide labels, d1
# see what it looks like ray traced
On Wed, May 12, 2010 at 6:37 AM, peter hudson
> Hello all
> i want draw axes or lines in my figure which corelates with structure and
> function relation of my protein structure. I have enclosed a sample figure.
> which would indicate , what exactly i want to draw in the picture. How to
> draw this in pymol? I would like the simple scripts.I would appreciate the
> suggestions. please, have look into the rrf.png file.
> Thanks in advance
> PyMOL-users mailing list (PyMOL-users@...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@...
Jason Vertrees, PhD
PyMOL Product Manager
(o) +1 (603) 374-7120
From: Robert Campbell <robert.campbell@qu...> - 2010-05-12 16:34:40
On Wed, 12 May 2010 10:42:36 -0400 Jason Vertrees
> If you knew the positions of the end points of the lines you could
> make CGO lines, or you could just use a distance measure between two
> pseudoatoms and modify some label/dash settings:
As Jason says, if you have some end-points you can make CGO lines (or
cylinders). I have a script to do that called draw_links.py on my
website. If you have two atoms to define the end-points you can just pick
them (so that they are called pk1 and pk2) and then run the command
It has options to control the colour and diameter of the cylinder, and you
can name the atoms rather than picking them. E.g.
draw_links prot1 & c. a & i. 105 & n. n, prot2 & c. b & i. 311 &
n. od1, radius=.2, color=blue
The color can also be specified as a tuple of numbers between 0 and 1 for the
r,g,b components and a second colour can be added if you want the colour of
the cylinder to fade from one end to the other.
draw_cylinder color=(.5,.2,.5), color2=pink, object_name=faded_links
(where pk1 and pk2 are the endpoints and faded_links will be the name of
the object created).
You can also use this to draw a bunch of CGO cylinders between pairs of
atoms. E.g. you want to show the domain motion after aligning parts of two
draw_links 1kfu & c. l & i. 105+262+286+288, 1kxr & c. a & i. 115+272+296+298,color1=red,color2=blue
If more than one atom is specified in each selection, then it will draw a
cylinder between each of the 4 pairs of C-alpha atoms specified in the two
selections. In this case the colour of the cylinder fades from red to blue,
but if you do not specify color2 then it will be a single colour.
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Botterell Hall Rm 644
Department of Biochemistry, Queen's University,
Kingston, ON K7L 3N6 Canada
Tel: 613-533-6821 Fax: 613-533-2497