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 <mhel...@cdrd.ca> 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 > PyMOL>run /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. _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
