[PyMOL] Starting PyMol in interactive IPython Session
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. However, when I want to
get the
coordinates of the structure the following happens: In [5]:
cmd.get_coords("1xyz") Out[5]: array([[ 41., 25., 36.], [ 40., 25.,
35.], [ 39., 24., 35.], ..., [ 11., 26., 67.], [ 4., 32., 95.], [ 22.,
45., 49.]], dtype=float32) Even though the datatype is float32
apparently the decimals got lost somehow. The coordinates of the first
atom should be: 41.511 25.152 36.876 Repeating the above in a normal
interactive Python Session everything works just fine:
>>> import pymol >>> from pymol import cmd >>> pymol.finish_launching() >>>
cmd.fetch("1xyz") >>> cmd.get_coords("1xyz") array([[ 41.51100159,
25.15200043, 36.87599945], [ 40.9070015 , 25.55500031, 35.56299973], [
39.68399811, 24.70700073, 35.10599899], ..., [ 11.8878, 26.97699928,
67.03900146], [ 4.45699978, 32.77299881, 95.16600037], [ 22.64100075,
45.7840004 , 49.03900146]], dtype=float32) As I use IPython only for
debugging of PyMol scripts/plugins this is not a very big problem. Still
I'm interested in what causes this strange behavior. Is it a problem/bug
in IPython or in PyMol? Maybe someone has more insights here and can
give clarity! Using Python 2.7.12, IPython 5.1.0 and PyMol 1.8.4.0
Thanks! regards Leonhard
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Re: [PyMOL] Starting PyMol in interactive IPython Session
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 [3]: pymol.finish_launching()
In [4]: cmd.fetch("1xyz")
So far, everything is normal.
However, when I want to get the coordinates of the structure the
following happens:
In [5]: cmd.get_coords("1xyz")
Out[5]:
array([[ 41., 25., 36.],
[ 40., 25., 35.],
[ 39., 24., 35.], ...,
[ 11., 26., 67.],
[ 4., 32., 95.],
[ 22., 45., 49.]], dtype=float32)
Even though the datatype is float32 apparently the decimals got lost
somehow.
The coordinates of the first atom should be: 41.511 25.152 36.876
Repeating the above in a normal interactive Python Session everything
works just fine:
>>> import pymol
>>> from pymol import cmd
>>> pymol.finish_launching()
>>> cmd.fetch("1xyz")
>>> cmd.get_coords("1xyz")
array([[ 41.51100159, 25.15200043, 36.87599945],
[ 40.9070015 , 25.55500031, 35.56299973],
[ 39.68399811, 24.70700073, 35.10599899], ...,
[ 11.8878, 26.97699928, 67.03900146],
[ 4.45699978, 32.77299881, 95.16600037],
[ 22.64100075, 45.7840004 , 49.03900146]], dtype=float32)
As I use IPython only for debugging of PyMol scripts/plugins this is not
a very big problem.
Still I'm interested in what causes this strange behavior. Is it a
problem/bug in IPython or in PyMol?
Maybe someone has more insights here and can give clarity!
Using Python 2.7.12, IPython 5.1.0 and PyMol 1.8.4.0
Thanks!
regards
Leonhard
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[PyMOL] Coordinates of an atom
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) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Coordinates of an atom
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 help me in how to get coordinates of a selected atom or
> residue?
>
>
>
> Thank you
>
>
>
> Mohsen
>
>
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>
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>
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Re: [PyMOL] Coordinates of an atom
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 how to get coordinates of a selected atom or > residue? > > > > Thank you > > > > Mohsen > > > -- > > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Starting PyMol in interactive IPython Session
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
> 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 [3]: pymol.finish_launching()
> In [4]: cmd.fetch("1xyz")
>
> So far, everything is normal.
> However, when I want to get the coordinates of the structure the following
> happens:
>
> In [5]: cmd.get_coords("1xyz")
> Out[5]:
> array([[ 41., 25., 36.],
> [ 40., 25., 35.],
> [ 39., 24., 35.], ...,
> [ 11., 26., 67.],
> [ 4., 32., 95.],
> [ 22., 45., 49.]], dtype=float32)
>
> Even though the datatype is float32 apparently the decimals got lost
> somehow.
> The coordinates of the first atom should be: 41.511 25.152 36.876
>
> Repeating the above in a normal interactive Python Session everything
> works just fine:
>
> >>> import pymol
> >>> from pymol import cmd
> >>> pymol.finish_launching()
> >>> cmd.fetch("1xyz")
> >>> cmd.get_coords("1xyz")
> array([[ 41.51100159, 25.15200043, 36.87599945],
> [ 40.9070015 , 25.55500031, 35.56299973],
> [ 39.68399811, 24.70700073, 35.10599899], ...,
> [ 11.8878, 26.97699928, 67.03900146],
> [ 4.45699978, 32.77299881, 95.16600037],
> [ 22.64100075, 45.7840004 , 49.03900146]], dtype=float32)
>
> As I use IPython only for debugging of PyMol scripts/plugins this is not a
> very big problem.
> Still I'm interested in what causes this strange behavior. Is it a
> problem/bug in IPython or in PyMol?
> Maybe someone has more insights here and can give clarity!
>
> Using Python 2.7.12, IPython 5.1.0 and PyMol 1.8.4.0
>
> Thanks!
>
> regards
> Leonhard
>
>
> --
>
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>
--
Tsjerk A. Wassenaar, Ph.D.
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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
>
>
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