Re: [PyMOL] Starting PyMol in interactive IPython Session

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 the _cmd.so C-lib also returns the
wrong coords:

>>> pymol._cmd.get_coords(cmd._COb, "1xyz")

array([[ 41., 25., 36.], [ 40., 25., 35.], [ 39., 24., 35.], ..., [ 11.,
26., 67.], [ 4., 32., 95.], [ 22., 45., 49.]], dtype=float32)

The error occurs both with local loaded pdb files and fetched pdb files.
(I initially supposed it had something to do with the fetch function of
the psicio plugin, which overloads the original fetch command)

So there must be something wrong with the loading of the pdb, when using
IPython...


regards

Leonhard


On 01.12.2016 16:35, Tsjerk Wassenaar wrote:
> 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
>
>