Hi Thomas!
Thanks for your answer. Your first suggestions works.
Regarding the comment on B4 I was importing cmd from pymol because
otherwise I get error
"name 'cmd' is not defined"
Cheers,
Osvaldo.
On Sun, Aug 24, 2014 at 8:01 PM, Thomas Holder <
[email protected]> wrote:
> Hi Osvaldo,
>
> A3) PyMOL captures sys.stdout, but you can reclaim it:
>
> import sys, pymol
> stdout = sys.stdout
> pymol.finish_launching()
> sys.stdout = stdout
>
> B4) "cmd" is your ServerProxy instance, so don't import anything "from
> pymol"
>
> Cheers,
> Thomas
>
> On 24 Aug 2014, at 13:36, Osvaldo Martin <[email protected]> wrote:
>
> > I was trying to use pymol within Ipython notebook, but I can get all the
> functionality of PyMOL and/or Ipython, let me explain.
> >
> > I tried the following two options:
> >
> > A) Like a normal script
> >
> > 1) I lauch PyMOL (inside the ipython notebook)
> > import pymol
> > from pymol import cmd, stored
> > pymol.finish_launching()
> >
> > 2) I do stuff like
> > cmd.load('mol.pdb')
> >
> > 3) I import custom python/pymol code without any problem
> >
> > The problem with this approach is that the output of commands like
> "cmd.get_area" are rendered inside the notebook, but the output of commands
> like "ls" are rendered inside PyMOL terminal.
> >
> > B) Like a remote connection
> >
> > 1) I lunch pymol using "pymol -R"
> > 2) I Lunch the XML-RPC server (inside the notebook) by doing
> >
> > from xmlrpclib import ServerProxy
> > cmd = ServerProxy(uri="http://localhost:9123/RPC2";)
> >
> > 3) I do stuff like
> > cmd.load('mol.pdb')
> >
> > 4) I try to import custom python/pymol code e.g somethin like
> >
> > from pymol import cmd, stored
> >
> > def get_phi(res_num):
> > if res_num != 0:
> > cmd.select('A', 'resi %s and name C' % (res_num-1))
> > cmd.select('B', 'resi %s and name N' % res_num)
> > cmd.select('C', 'resi %s and name CA' % res_num)
> > cmd.select('D', 'resi %s and name C' % res_num)
> > return cmd.get_dihedral('A', 'B', 'C', 'D')
> > else:
> > return float('nan')
> >
> > and I get the error "'module' object has no attribute 'glutThread'",
> normally this will be fixed by adding the line 'pymol.finish_launching()',
> but If I do that Ipython get locked (waiting to launch a new PyMOL session).
>
> --
> Thomas Holder
> PyMOL Developer
> Schrödinger, Inc.
>
>
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