On Wed, Jun 11, 2008 at 11:48 AM, David Goldenberg < goldenb...@biology.utah.edu> wrote:
> > Now, could someone point me in the right direction (so to speak) > regarding translations of a molecule relative to the graphics reference > frame? > By default, the translate command works in relation to the camera view. To use the model's geometry instead, set the "camera" option to 0: translate [1,0,0] vs. translate [1,0,0],camera=0 -michael > > Thanks again, > David > > Tsjerk Wassenaar wrote: > > 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 > >> > > > > > > > > -- > 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 > -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909 Rockville, MD 20852 http://www.umich.edu/~mlerner
