Re: [PyMOL] Compiling open source pymol 2.4

Agreed, Thomas.

Thanks for your help!

> -----Original Message-----
> From: Thomas Holder <tho...@sc...>
> Sent: Tuesday, March 12, 2019 12:14 PM
> To: Markus Heller <mh...@cd...>
> Cc: pym...@li...
> Subject: Re: [PyMOL] Compiling open source pymol 2.4
> 
> Hi Markus,
> 
> I recommend to use Python 3. The PyMOLWiki has updated versions of those
> two failing scripts:
> 
> https://pymolwiki.org/index.php/Pairwise_distances
> https://pymolwiki.org/index.php/Polarpairs
> 
> I don't know why there would be no menu bar with Python 2.7. But if Python 3
> works for you, I think there is no need to figure that out.
> 
> Cheers,
>   Thomas
> 
> > On Mar 12, 2019, at 7:34 PM, Markus Heller <mh...@cd...> wrote:
> >
> > Hi all,
> >
> > I'm having trouble compiling open source Pymol 2.4.
> >
> > If I compile with python 2.7, the compilation finishes without errors or
> warnings, but when I start Pymol, I don't see the menu bar at the top of the
> window, and I don't see any errors.
> >
> > If, on the other hand, I compile with python 3, Pymol starts and I see the menu
> bar, but I get warnings in the Pymol console that are related to a version conflict
> of python 3 used for compilation and python 2 used in some scripts, e.g. the
> ones shown below.
> >
> > What's the python version to use for compiling, and how do I best proceed?
> >
> > Thanks
> > Markus
> >
> > This is part of the output shown in the Pymol console on startup:
> >
> > PyMOL>run /home/mheller/.pymol/show_bumps.py
> > PyMOL>run /home/mheller/.pymol/pairwisedistances.py
> > Traceback (most recent call last):
> >  File "/home/mheller/pymol-2.4/lib/python/pymol/parsing.py", line 483, in run
> >    run_(path, ns_pymol, ns_pymol)
> >  File "/home/mheller/pymol-2.4/lib/python/pymol/parsing.py", line 532, in
> run_file
> >    execfile(file,global_ns,local_ns)
> >  File "/home/mheller/pymol-2.4/lib/python/pymol/parsing.py", line 526, in
> execfile
> >    co = compile(pi.file_read(filename), filename, 'exec')  File
> > "/home/mheller/.pymol/pairwisedistances.py", line 13
> >    print ""
> >           ^
> > SyntaxError: Missing parentheses in call to 'print'. Did you mean print("")?
> > PyMOL>run /home/mheller/.pymol/supercell.py run
> > PyMOL>/home/mheller/.pymol/get_raw_distances.py
> > PyMOL>run /home/mheller/.pymol/polarpairs.py
> > Traceback (most recent call last):
> >  File "/home/mheller/pymol-2.4/lib/python/pymol/parsing.py", line 483, in run
> >    run_(path, ns_pymol, ns_pymol)
> >  File "/home/mheller/pymol-2.4/lib/python/pymol/parsing.py", line 532, in
> run_file
> >    execfile(file,global_ns,local_ns)
> >  File "/home/mheller/pymol-2.4/lib/python/pymol/parsing.py", line 526, in
> execfile
> >    co = compile(pi.file_read(filename), filename, 'exec')  File
> > "/home/mheller/.pymol/polarpairs.py", line 39
> >    print 'Settings: cutoff=%.1fangstrom angle=%.1fdegree' % (cutoff, angle)
> >                                                         ^
> > SyntaxError: invalid syntax
> 
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.