Re: [PyMOL] AutoDock plugin

[James S. <jms...@gm...>]

Thomas,

Thanks for suggestions.

1)I have installed Numpy.

2)   File "/usr/lib/python2.7/dist-packages/pymol/parser.py", line 260, in
parse
    exec(layer.com2+"\n",self.pymol_names,self.pymol_names)
  File "<string>", line 1, in <module>
  File "/usr/share/pyshared/pmg_tk/startup/autodock_plugin.py", line 62, in
<module>
    from numpy import *
  File "/usr/share/pyshared/numpy/__init__.py", line 137, in <module>
    import add_newdocs
  File "/usr/share/pyshared/numpy/add_newdocs.py", line 9, in <module>
    from numpy.lib import add_newdoc
  File "/usr/share/pyshared/numpy/lib/__init__.py", line 4, in <module>
    from type_check import *
  File "/usr/share/pyshared/numpy/lib/type_check.py", line 8, in <module>
    import numpy.core.numeric as _nx
  File "/usr/share/pyshared/numpy/core/__init__.py", line 5, in <module>
    import multiarray
ImportError: No module named multiarray


What  package is needed which consist of multiarray module ?

James


2013/12/6 Thomas Holder <sp...@us...>

> Hi James,
>
> import pmg_tk.startup.autodock_plugin
>
> should tell you what's wrong. My next guess is that you don't have numpy
> installed.
>
> For the missing bonds in your example, PyMOL thinks those atoms are
> cations because of the symbol in the last column. By default, PyMOL doesn't
> make bonds to cations. But this will work:
>
> PyMOL>unset pdb_unbond_cations,
> PyMOL>load example.pdb
>
> Hope that helps.
>
> Cheers,
>   Thomas
>
> On 06 Dec 2013, at 11:04, James Starlight <jms...@gm...> wrote:
>
> > Thomas,
> >
> > I have this problem within the recent pymol 1.6.0.0 version installed on
> Linux Debian (all others plugins work correct. Also Autodock plugin is not
> seen in the repository)
> >
> > By the way in this Pymol version I've forced with some problems with the
> ligands representation. For example I've obtained typical docking output
> from the AutoDock consisted of 10 poses (in separate models) but some atoms
> of this ligands is visualized as a blank atoms. Below the atoms of the one
> model are provided as the example.
> >
> > HETATM    1  CAG P0G R   1      -0.073  -2.031  12.923  1.00  0.00
>  .001 A
> > HETATM    2  CAH P0G R   1      -0.624  -2.630  11.797  1.00  0.00
>  .001 A
> > HETATM    3  CAI P0G R   1       0.713  -0.894  12.787  1.00  0.00
>  .007 A
> > HETATM    4  CAJ P0G R   1      -0.383  -2.091  10.540  1.00  0.00
>  .007 A
> > HETATM    5  CAW P0G R   1      -2.339   3.404   5.677  1.00  0.00
>  .008 A
> > HETATM    6  CAL P0G R   1      -1.712   3.845   4.518  1.00  0.00
>  .015 A
> > HETATM    7  CAK P0G R   1      -1.825   5.176   4.131  1.00  0.00
>  .039 A
> > HETATM    8  CAB P0G R   1       0.291   2.102   8.752  1.00  0.00
>  .046 C
> > HETATM    9  CAC P0G R   1      -1.618   0.656   9.433  1.00  0.00
>  .046 C
> > HETATM   10  CAA P0G R   1       1.806   0.879  11.409  1.00  0.00
>  .049 C
> > HETATM   11  CAV P0G R   1       0.396  -0.946  10.403  1.00  0.00
>  .050 A
> > HETATM   12  CAT P0G R   1       0.950  -0.354  11.529  1.00  0.00
>  .056 A
> > HETATM   13  NAP P0G R   1      -0.642   0.506   7.208  1.00  0.00
>  .064 N
> > HETATM   14  CAO P0G R   1       0.652  -0.375   9.023  1.00  0.00
>  .077 C
> > HETATM   15  CAU P0G R   1      -2.570   6.062   4.900  1.00  0.00
>  .095 A
> > HETATM   16  CAX P0G R   1      -3.197   5.612   6.048  1.00  0.00
>  .102 A
> > HETATM   17  CAY P0G R   1      -3.084   4.294   6.426  1.00  0.00
>  .107 A
> > HETATM   18  CBA P0G R   1      -0.335   0.720   8.612  1.00  0.00
>  .122 C
> > HETATM   19  HAQ P0G R   1      -3.677   7.418   6.890  1.00  0.00
>  .169 H
> > HETATM   20  CAZ P0G R   1      -2.233   1.990   6.093  1.00  0.00
>  .179 C
> > HETATM   21  HAF P0G R   1      -2.600   0.245   5.251  1.00  0.00
>  .210 H
> > HETATM   22  HAE P0G R   1      -2.798   7.416   3.572  1.00  0.00
>  .217 H
> > HETATM   23  CAS P0G R   1      -4.971   5.977   7.513  1.00  0.00
>  .246 C
> > HETATM   24  CAN P0G R   1      -0.768   1.610   6.272  1.00  0.00
>  .269 C
> > HETATM   25  OAD P0G R   1      -5.901   6.691   7.854  1.00  0.00
>  .271 O
> > HETATM   26  CAM P0G R   1      -4.980   4.505   7.870  1.00  0.00
>  .278 C
> > HETATM   27 2HAP P0G R   1      -1.522   0.012   7.182  1.00  0.00
>  .278 H
> > HETATM   28 3HAP P0G R   1       0.062  -0.118   6.840  1.00  0.00
>  .278 H
> > HETATM   29  NAQ P0G R   1      -3.925   6.442   6.827  1.00  0.00
>  .321 N
> > HETATM   30  OAR P0G R   1      -3.718   3.912   7.572  1.00  0.00
>  .339 O
> > HETATM   31  OAE P0G R   1      -2.682   7.366   4.523  1.00  0.00
>  .358 O
> > HETATM   32  OAF P0G R   1      -2.799   1.167   5.067  1.00  0.00
>  .389 O
> >
> >
> > 2013/12/6 Thomas Holder <sp...@us...>
> > Hi James,
> >
> > is it recent version of PyMOL, or recent version of Windows which makes
> trouble? On Windows, the plugin tries to write to the PyMOL installation
> folder, which fails if you don't have write permissions there. This needs
> to be fixed, the plugin should write to the users folder also on Windows.
> >
> > Cheers,
> >   Thomas
> >
> > On 06 Dec 2013, at 08:47, James Starlight <jms...@gm...>
> wrote:
> >
> > > Dear PyMol users!
> > >
> > > I've forced with the problem of the installation of AutoDock plugin
> pymoawiki.org/index.php/Autodock_plugin  in recent pymol version. I've
> tried to install it manually from the downloaded py script but at the
> starting of pymol below error has bbeen appeared
> > >
> > > Unable to initialize plugin 'autodock' (pmg_tk.startup.autodock).
> > > Unable to initialize plugin 'autodock_plugin'
> (pmg_tk.startup.autodock_plugin).
> > >
> > > Also I've tried to search for the plugin in the pymol repositories but
> have not found it. How it could be solved ?
> > >
> > > James
>