Hi Edmund,
Actually, PyMOL uses a set of stored coordinates for fragments
and residues. They can be found in $PYMOL_PATH/data/chempy/fragments.
The files have .pkl extensions, which stands for pickled chempy model.
These files can be viewed directly in PyMOL, or can be introspected by
unp
Rob,
There isn't a public API function which does this at present but
the private _cmd.get_pdb call does exactly that. To see an example of
how it is used, look at the "save" function in
modules/pymol/exporting.py. I'll add a cmd.get_pdbstr() function to the
next version of PyMOL, since
Hi All,
I am a very new user of pymol. I just started yesterday. I have
installed the 0.9 version for mac. When I start the program, the menu
bar on the graphics window does not appear. I know that everything is
possible with the command line but since I am a new user, I would
prefer to see th
On Wed, Sep 10, 2003 at 10:57:59AM +0300, Dr. Daniel James White PhD wrote:
> Warren ,
>
> Are you aware of the python MMTK molecular dynamics package?
> AMBER force field and energy minimisation are there!
> Could this be easily interfaced with pymol?
>
> http://starship.python.net/crew/hinsen/M
hi,
i've succesfully done transparent cartoons, combining PyMOL and ADOBE
PHOTOSHOP.
here goes my tip:
on PyMOL:
1 - ray-trace and save your picture without cartoons (with your favorite
color style);
2 - now, load the cartoons (with colors you want), and paint the
previous molecule (without c
Greetings,
I am interested in modifying how pymol generates the coordinates of
atoms in a peptide chain as you add residues to it. I am an
undergraduate math student, so my knowledge in this area is in the
range of "nothing". I would assume that this would be in the bonding
or editor modules
