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