Re: [PyMOL] Compiling open source pymol 2.4
Agreed, Thomas.
Thanks for your help!
> -Original Message-
> From: Thomas Holder
> Sent: Tuesday, March 12, 2019 12:14 PM
> To: Markus Heller
> Cc: pymol-users@lists.sourceforge.net
> 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 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.
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Re: [PyMOL] Compiling open source pymol 2.4
Hi Markus,
I can answer part of your question.
There are error messages about print statement in python2 needing to be
converted to print() functions for python3.
You can run the program 2to3 on your python scripts to convert them from python2
to python3. This program probably came with your one of the Python's on your
machine.
It is not perfect. You might have to follow up with some manual edits.
Best regards,
Blaine
Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
From: Markus Heller [mhel...@cdrd.ca]
Sent: Tuesday, March 12, 2019 1:34 PM
To: pymol-users@lists.sourceforge.net
Subject: [EXTERNAL] [PyMOL] Compiling open source pymol 2.4
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/https://urldefense.proofpoint.com/v2/url?u=http-3A__show-5Fbumps.py=DwICAg=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=m0TqOpm-acg2I6R7GInhCKREAQggkxgFI3UGfclNs8g=bs-lPs-R0puQhuGq2S89IblUxdRGrAxvt7D_LqSLYBo=
PyMOL>run
/home/mheller/.pymol/https://urldefense.proofpoint.com/v2/url?u=http-3A__pairwisedistances.py=DwICAg=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=m0TqOpm-acg2I6R7GInhCKREAQggkxgFI3UGfclNs8g=C0opkKUhEfyNxDi0bpCC9w3s30eP0fV8eKhv8lemrVw=
Traceback (most recent call last):
File
"/home/mheller/pymol-2.4/lib/python/pymol/https://urldefense.proofpoint.com/v2/url?u=http-3A__parsing.py=DwICAg=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=m0TqOpm-acg2I6R7GInhCKREAQggkxgFI3UGfclNs8g=UwuMSV6A6OB1jIngETqXpMT5HPhn_p6IHCLoVp5KNPQ=;,
line 483, in run
run_(path, ns_pymol, ns_pymol)
File
"/home/mheller/pymol-2.4/lib/python/pymol/https://urldefense.proofpoint.com/v2/url?u=http-3A__parsing.py=DwICAg=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=m0TqOpm-acg2I6R7GInhCKREAQggkxgFI3UGfclNs8g=UwuMSV6A6OB1jIngETqXpMT5HPhn_p6IHCLoVp5KNPQ=;,
line 532, in run_file
execfile(file,global_ns,local_ns)
File
"/home/mheller/pymol-2.4/lib/python/pymol/https://urldefense.proofpoint.com/v2/url?u=http-3A__parsing.py=DwICAg=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=m0TqOpm-acg2I6R7GInhCKREAQggkxgFI3UGfclNs8g=UwuMSV6A6OB1jIngETqXpMT5HPhn_p6IHCLoVp5KNPQ=;,
line 526, in execfile
co = compile(pi.file_read(filename), filename, 'exec')
File
"/home/mheller/.pymol/https://urldefense.proofpoint.com/v2/url?u=http-3A__pairwisedistances.py=DwICAg=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=m0TqOpm-acg2I6R7GInhCKREAQggkxgFI3UGfclNs8g=C0opkKUhEfyNxDi0bpCC9w3s30eP0fV8eKhv8lemrVw=;,
line 13
print ""
^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print("")?
PyMOL>run
/home/mheller/.pymol/https://urldefense.proofpoint.com/v2/url?u=http-3A__supercell.py=DwICAg=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=m0TqOpm-acg2I6R7GInhCKREAQggkxgFI3UGfclNs8g=1cEHfd8ZYNLzS3SDZf3MA3JXMrWqQ46U7dgLaBVEyHU=
PyMOL>run
/home/mheller/.pymol/https://urldefense.proofpoint.com/v2/url?u=http-3A__get-5Fraw-5Fdistances.py=DwICAg=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=m0TqOpm-acg2I6R7GInhCKREAQggkxgFI3UGfclNs8g=uU2XHleaq91jTq-TtUuewYn7hUxfCFtCE2C89CKutLs=
PyMOL>run
/home/mheller/.pymol/https://urldefense.proofpoint.com/v2/url?u=http-3A__polarpairs.py=DwICAg=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=m0TqOpm-acg2I6R7GInhCKREAQggkxgFI3UGfclNs8g=2opEfhq5bNu2N5-W8xtazkiK7_XQEA85VwlCLVO-LrY=
Traceback (most recent call last):
File
"/home/mheller/pymol-2.4/lib/python/pymol/https://urldefense.proofpoint.com/v2/url?u=http-3A__parsing.py=DwICAg=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=m0TqOpm-acg2I6R7GInhCKREAQggkxgFI3UGfclNs8g=UwuMSV6A6OB1jIngETqXpMT5HPhn_p6IHCLoVp5KNPQ=;,
line 483, in run
run_(path, ns_pymol, ns_py
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 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.
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[PyMOL] Compiling open source pymol 2.4
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
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