Hi David, Regarding the first part of your question, the way to load a python (not a PyMol) script is:
run axes.py .. and not @axes.py. The latter is used for loading PyMol scripts (.pml). You _can_ use python code in a .pml script, but then you better, or in some cases have to, start with a slash (/) to let the command parser know that there's python code coming. Hope it helps, Tsjerk On Wed, Jun 11, 2008 at 12:10 AM, David Goldenberg <goldenb...@biology.utah.edu> wrote: > Hi, > I would like to make a figure that shows a set of coordinate axes > aligned in a particular way with respect to a molecule. I have found > the axes.py script (copied at the bottom of this message) on the PyMol > Wiki, but have run into the following problems: > > 1. I can't get the script to load and run properly in MacPymol. I get a > long string of error messages beginning with: > > PyMOL>@axes.py > PyMOL>from pymol.cgo import * > PyMOL>from pymol import cmd > PyMOL>from pymol.vfont import plain > PyMOL>obj = [ > Traceback (most recent call last): > File "/Applications/Molecular > Graphics/MacPyMOL.app/pymol/modules/pymol/parser.py", line 208, in parse > exec(layer.com2+"\n",self.pymol_names,self.pymol_names) > File "<string>", line 1 > obj = [ > ^ > SyntaxError: unexpected EOF while parsing > > I can get the script to run with an old version (0.98) of the Mac-X11 > hybrid. I can live with this, if necessary. > > 2. Once I have the axes and the molecule loaded, I would like to place a > particular atom at the origin and then rotate the molecule into a > particular orientation. I thought that I could do the first part by > using the translate command, by moving the molecule by amounts that > correspond to the negative of the initial coordinates of the atom of > interest. That is, if the initial coordinates (from the pdb file) are, > 1,-2,2, it seems that if I do > translate [-1,2,-2] > I should move the molecule so that the atom is at the origin. But, this > doesn't happen; The molecule moves, but not along the expected axes. > There is clearly something about the coordinate system and the translate > command that I don't understand. > > Any suggestions for how to go about this would be greatly appreciated! > > David > > > ---------------- > > The script: > > # 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') > > -- > Department of Biology > University of Utah > 257 South 1400 East > Salt Lake City, UT 84112-0840 > > Telephone: (801) 581-3885 > Fax: (801) 581-2174 > > E-mail: goldenb...@biology.utah.edu > Lab web page: http://www.biology.utah.edu/goldenberg > > ------------------------------------------------------------------------- > Check out the new SourceForge.net Marketplace. > It's the best place to buy or sell services for > just about anything Open Source. > http://sourceforge.net/services/buy/index.php > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623
