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&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=m0TqOpm-acg2I6R7GInhCKREAQggkxgFI3UGfclNs8g&s=bs-lPs-R0puQhuGq2S89IblUxdRGrAxvt7D_LqSLYBo&e= PyMOL>run /home/mheller/.pymol/https://urldefense.proofpoint.com/v2/url?u=http-3A__pairwisedistances.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=m0TqOpm-acg2I6R7GInhCKREAQggkxgFI3UGfclNs8g&s=C0opkKUhEfyNxDi0bpCC9w3s30eP0fV8eKhv8lemrVw&e= 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&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=m0TqOpm-acg2I6R7GInhCKREAQggkxgFI3UGfclNs8g&s=UwuMSV6A6OB1jIngETqXpMT5HPhn_p6IHCLoVp5KNPQ&e=";, 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&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=m0TqOpm-acg2I6R7GInhCKREAQggkxgFI3UGfclNs8g&s=UwuMSV6A6OB1jIngETqXpMT5HPhn_p6IHCLoVp5KNPQ&e=";, 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&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=m0TqOpm-acg2I6R7GInhCKREAQggkxgFI3UGfclNs8g&s=UwuMSV6A6OB1jIngETqXpMT5HPhn_p6IHCLoVp5KNPQ&e=";, 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&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=m0TqOpm-acg2I6R7GInhCKREAQggkxgFI3UGfclNs8g&s=C0opkKUhEfyNxDi0bpCC9w3s30eP0fV8eKhv8lemrVw&e=";, 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&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=m0TqOpm-acg2I6R7GInhCKREAQggkxgFI3UGfclNs8g&s=1cEHfd8ZYNLzS3SDZf3MA3JXMrWqQ46U7dgLaBVEyHU&e= PyMOL>run /home/mheller/.pymol/https://urldefense.proofpoint.com/v2/url?u=http-3A__get-5Fraw-5Fdistances.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=m0TqOpm-acg2I6R7GInhCKREAQggkxgFI3UGfclNs8g&s=uU2XHleaq91jTq-TtUuewYn7hUxfCFtCE2C89CKutLs&e= PyMOL>run /home/mheller/.pymol/https://urldefense.proofpoint.com/v2/url?u=http-3A__polarpairs.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=m0TqOpm-acg2I6R7GInhCKREAQggkxgFI3UGfclNs8g&s=2opEfhq5bNu2N5-W8xtazkiK7_XQEA85VwlCLVO-LrY&e= 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&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=m0TqOpm-acg2I6R7GInhCKREAQggkxgFI3UGfclNs8g&s=UwuMSV6A6OB1jIngETqXpMT5HPhn_p6IHCLoVp5KNPQ&e=";, 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&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=m0TqOpm-acg2I6R7GInhCKREAQggkxgFI3UGfclNs8g&s=UwuMSV6A6OB1jIngETqXpMT5HPhn_p6IHCLoVp5KNPQ&e=";, 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&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=m0TqOpm-acg2I6R7GInhCKREAQggkxgFI3UGfclNs8g&s=UwuMSV6A6OB1jIngETqXpMT5HPhn_p6IHCLoVp5KNPQ&e=";, 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__polarpairs.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=m0TqOpm-acg2I6R7GInhCKREAQggkxgFI3UGfclNs8g&s=2opEfhq5bNu2N5-W8xtazkiK7_XQEA85VwlCLVO-LrY&e=";, line 39 print 'Settings: cutoff=%.1fangstrom angle=%.1fdegree' % (cutoff, angle) ^ SyntaxError: invalid syntax _______________________________________________ PyMOL-users mailing list Archives: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=m0TqOpm-acg2I6R7GInhCKREAQggkxgFI3UGfclNs8g&s=61FtPZoFPqjTfe1UVJP_g0zqojGHScsh50AFpxinGJo&e= Unsubscribe: https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=m0TqOpm-acg2I6R7GInhCKREAQggkxgFI3UGfclNs8g&s=OFu16kizGxHbOsTZOAVaqf1j0eMQPSKph0iAeT743iM&e= _______________________________________________ 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
