Hi!
I stumbled upon some odd behavior when starting PyMol in an interactive
IPython Session.
PyMol can be launched from interactive IPython like this:
In [1]: import pymol
In [2]: from pymol import cmd
In [3]: pymol.finish_launching()
In [4]: cmd.fetch("1xyz")So far, everything is normal. Howeve
I guess formatting didn't work out as i expected. So once again and
hopefully formatted:
Hi!
I stumbled upon some odd behavior when starting PyMol in an interactive
IPython Session.
PyMol can be launched from interactive IPython like this:
In [1]: import pymol
In [2]: from pymol import cmd
In [
Hi all,
Can anyone please help me in how to get coordinates of a selected atom or
residue?
Thank you
Mohsen
--
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Hej,
try this command and specify the atom selection:
cmd.get_atom_coords('atom selection')
see also:
https://pymolwiki.org/index.php/Get_Coordinates_I
Cheers,
Andreas
On Thu, Dec 1, 2016 at 2:19 PM, Mohsen Chitsaz <
mohsen.chit...@flinders.edu.au> wrote:
> Hi all,
>
>
>
> Can anyone please
Dear Mohsen,
when I Google "pymol coordinates atom", the top hit is this:
https://pymolwiki.org/index.php/Get_Coordinates_I
Worth a try.
All best.
Andreas
On Thu, Dec 1, 2016 at 2:19 PM, Mohsen Chitsaz <
mohsen.chit...@flinders.edu.au> wrote:
> Hi all,
>
>
>
> Can anyone please help me in
Hi Leonhard,
I would guess it's the formatting setting of numpy in IPython. You can see
what one float really is:
print(cmd.get_coords("1xyz")[0,0])
Cheers,
Tsjerk
On Thu, Dec 1, 2016 at 1:40 PM, Leonhard Heizinger wrote:
> I guess formatting didn't work out as i expected. So once again and
Hi Tsjerk,
thanks for your reply!
this was also my first guess. However it isn't a formatting issue:
In [5]: print(cmd.get_coords("1xyz")[0,0])
41.0
Also fetched structures look "teared" in cartoon representation,
supposedly because of the wrong coordinates.
Calling the internal function from
