On Wed, Jun 11, 2008 at 11:48 AM, David Goldenberg <goldenberg@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
> <goldenberg@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: goldenberg@biology.utah.edu
>> Lab web page: http://www.biology.utah.edu/goldenberg
>>
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>
>
>

--
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: goldenberg@biology.utah.edu
Lab web page: http://www.biology.utah.edu/goldenberg

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