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 <speleo3@users.sourceforge.net>
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 <jmsstarlight@gmail.com> 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 <speleo3@users.sourceforge.net>
> 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 <jmsstarlight@gmail.com> 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