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
