Hi Peter, On Wed, 12 May 2010 10:42:36 -0400 Jason Vertrees <jason.vertr...@schrodinger.com> wrote:
> Peter, > > 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 draw_links 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 structures: 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. Cheers, Rob -- 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 <robert.campb...@queensu.ca> http://pldserver1.biochem.queensu.ca/~rlc ------------------------------------------------------------------------------ _______________________________________________ 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
