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 <spel...@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 <jmsstarli...@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 <spel...@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 <jmsstarli...@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
>
------------------------------------------------------------------------------
Sponsored by Intel(R) XDK
Develop, test and display web and hybrid apps with a single code base.
Download it for free now!
http://pubads.g.doubleclick.net/gampad/clk?id=111408631&iu=/4140/ostg.clktrk
_______________________________________________
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
