* Tommy Wang <chern...@ima.org.sg> [2002-05-10 19:52] wrote: > How do I view the direction vectors i.e. x,y,z in pymol? >
This is how I would do it. Create a python script (I call it axes.py): # axes.py from pymol.cgo import * from pymol import cmd from pymol.vfont import plain # create the axes object, draw axes with cylinders coloured red, green, #blue for X, Y and Z obj = [ CYLINDER, 0., 0., 0., 10., 0., 0., 0.2, 1.0, 1.0, 1.0, 1.0, 0.0, 0., CYLINDER, 0., 0., 0., 0., 10., 0., 0.2, 1.0, 1.0, 1.0, 0., 1.0, 0., CYLINDER, 0., 0., 0., 0., 0., 10., 0.2, 1.0, 1.0, 1.0, 0., 0.0, 1.0, ] # add labels to axes object (requires pymol version 0.8 or greater, I # believe cyl_text(obj,plain,[-5.,-5.,-1],'Origin',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]]) cyl_text(obj,plain,[10.,0.,0.],'X',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]]) cyl_text(obj,plain,[0.,10.,0.],'Y',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]]) cyl_text(obj,plain,[0.,0.,10.],'Z',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]]) # then we load it into PyMOL cmd.load_cgo(obj,'axes') ################### end of script Then you just need to do "run axes.py" from the pymol command line. You can modify the "3" in the above description of the text labels to change the size of the labels. If you are running a version of pymol older the 0.8, then you cannot add the text (that's why I included colour coding of the axes). You can also use just lines instead of cylinders if you wish: obj = [ BEGIN, LINES, COLOR, 1.0, 0.0, 0.0, VERTEX, 0.0, 0.0, 0.0, VERTEX, 10.0, 0.0, 0.0, COLOR, 0.0, 1.0, 0.0, VERTEX, 0.0, 0.0, 0.0, VERTEX, 0.0, 10.0, 0.0, COLOR, 0.0, 0.0, 1.0, VERTEX, 0.0, 0.0, 0.0, VERTEX, 0.0, 0.0, 10.0, END, ] would work as well to define the axes object. Cheers, Robert -- Robert L. Campbell, Ph.D. http://biophysics.med.jhmi.edu/rlc r...@k2.med.jhmi.edu phone: 410-614-6313 Research Specialist/X-ray Facility Manager HHMI/Dept. of Biophysics & Biophysical Chem., The Johns Hopkins University PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2
