Koray, Use cmd.get_distance when you have two atoms:
x = cmd.get_distance("10/CA", "11/CA") print x To script a solution to your problem I'd do: # # If your first selection (from residue A) is called "yourFirstSele" # and your second selection (from resisude B) is called, "yourSecondSele" # then the following script will print out the distances from atoms in the first # residue to those in the 2nd. # from pymol import stored stored.listA = [] stored.listB = [] iterate yourFirstSele, stored.listA.append(ID) iterate yourSecondSele, stored.listB.append(ID) python for aa in stored.listA: for bb in stored.listB: print "Distance from atom %d to atom %d is %f" % (aa,bb,cmd.get_distance("ID %d" % aa, "ID %d"% bb)) python end Feel free to modify that as necessary. Cheers, -- Jason On Thu, Mar 18, 2010 at 8:07 AM, koray <kki...@gwdg.de> wrote: > Hi, > > I created bond objects between residues I want to observe. > Now I have 35 bond objects. I want to color them based on the bond length. > But for that I should get the distance information of the bond object. If I > say show label, it shows the leght of the bond. > Is there a way to get this info by a command > I tried cmd.get_distance(Bond1) > but it is not working. > Thanks in advance > > Koray KIRLI > MPI / Goettingen > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > 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 > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ 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