Problem in call to pymol

[MooersLab]

I think that the way SUPERPOSITION.py calls pymol may be problematic on Mac OS X, probably due to the global interpreter lock.

Note that py37 is a an alias to 'sudo -H /opt/local/bin/python3.7'. I have pymol 3.3.0 for python3.7 installed via macports.

blaine2018mbp:Theseus-PP blaine$ py37 ./Calling_SUPERPOSITION.py
 PyMOL(TM) Molecular Graphics System, Version 2.3.0.
 Copyright (c) Schrodinger, LLC.
 All Rights Reserved.

    Created by Warren L. DeLano, Ph.D.

    PyMOL is user-supported open-source software.  Although some versions
    are freely available, PyMOL is not in the public domain.

    If PyMOL is helpful in your work or study, then please volunteer
    support for our ongoing efforts to create open and affordable scientific
    software by purchasing a PyMOL Maintenance and/or Support subscription.

    More information can be found at "http://www.pymol.org".

    Enter "help" for a list of commands.
    Enter "help <command-name>" for information on a specific command.

 Hit ESC anytime to toggle between text and graphics.

2019-09-29 22:20:25.571 Python[77112:5991956] *** Terminating app due to uncaught exception 'NSInternalInconsistencyException', reason: 'NSWindow drag regions should only be invalidated on the Main Thread!'
*** First throw call stack:
(
    0   CoreFoundation                      0x00007fff5317ba7d __exceptionPreprocess + 256
    1   libobjc.A.dylib                     0x00007fff7d851a17 objc_exception_throw + 48
    2   CoreFoundation                      0x00007fff531955d9 -[NSException raise] + 9
    3   AppKit                              0x00007fff5073b5ca -[NSWindow(NSWindow_Theme) _postWindowNeedsToResetDragMarginsUnlessPostingDisabled] + 317
    4   AppKit                              0x00007fff507389f7 -[NSWindow _initContent:styleMask:backing:defer:contentView:] + 1479
    5   AppKit                              0x00007fff5073842a -[NSWindow initWithContentRect:styleMask:backing:defer:] + 45
    6   AppKit                              0x00007fff50a04d08 -[NSWindow initWithContentRect:styleMask:backing:defer:screen:] + 52
    7   libqcocoa.dylib                     0x000000012e7577a5 qt_plugin_instance + 137938
    8   libqcocoa.dylib                     0x000000012e747cc4 qt_plugin_instance + 73713
    9   libqcocoa.dylib                     0x000000012e742219 qt_plugin_instance + 50502
    10  libqcocoa.dylib                     0x000000012e741cee qt_plugin_instance + 49179
    11  QtGui                               0x000000012b0d7e6b _ZN14QWindowPrivate6createEby + 145
    12  QtWidgets                           0x000000012bfc2385 _ZN14QWidgetPrivate10create_sysEybb + 1063
    13  QtWidgets                           0x000000012bfc1452 _ZN7QWidget6createEybb + 288
    14  QtWidgets                           0x000000012c0e14be _ZN8QMenuBar7hoveredEP7QAction + 884
    15  QtWidgets                           0x000000012c0e1222 _ZN8QMenuBar7hoveredEP7QAction + 216
    16  QtWidgets                           0x000000012c0b0e30 _ZNK11QMainWindow7menuBarEv + 70
    17  QtWidgets.so                        0x000000012c58817a _ZL24meth_QMainWindow_menuBarP7_objectS0_ + 87
    18  Python                              0x0000000106ef7b57 _PyMethodDef_RawFastCallKeywords + 235
    19  Python                              0x0000000106ef71de _PyCFunction_FastCallKeywords + 44
    20  Python                              0x0000000106f8c0ca call_function + 636
    21  Python                              0x0000000106f849be _PyEval_EvalFrameDefault + 3295
    22  Python                              0x0000000106f8c9ee _PyEval_EvalCodeWithName + 1870
    23  Python                              0x0000000106ef6e11 _PyFunction_FastCallDict + 441
    24  Python                              0x0000000106ef7f55 _PyObject_Call_Prepend + 150
    25  Python                              0x0000000106f358c1 slot_tp_init + 80
    26  Python                              0x0000000106f32564 type_call + 172
    27  Python                              0x0000000106ef7044 _PyObject_FastCallKeywords + 358
    28  Python                              0x0000000106f8c138 call_function + 746
    29  Python                              0x0000000106f84a49 _PyEval_EvalFrameDefault + 3434
    30  Python                              0x0000000106ef75b8 function_code_fastcall + 112
    31  Python                              0x0000000106f8c13f call_function + 753
    32  Python                              0x0000000106f849be _PyEval_EvalFrameDefault + 3295
    33  Python                              0x0000000106f8c9ee _PyEval_EvalCodeWithName + 1870
    34  Python                              0x0000000106ef6e11 _PyFunction_FastCallDict + 441
    35  Python                              0x0000000106f84c65 _PyEval_EvalFrameDefault + 3974
    36  Python                              0x0000000106ef75b8 function_code_fastcall + 112
    37  Python                              0x0000000106f8c13f call_function + 753
    38  Python                              0x0000000106f849a5 _PyEval_EvalFrameDefault + 3270
    39  Python                              0x0000000106ef75b8 function_code_fastcall + 112
    40  Python                              0x0000000106f8c13f call_function + 753
    41  Python                              0x0000000106f849a5 _PyEval_EvalFrameDefault + 3270
    42  Python                              0x0000000106ef75b8 function_code_fastcall + 112
    43  Python                              0x0000000106ef7f55 _PyObject_Call_Prepend + 150
    44  Python                              0x0000000106ef72eb PyObject_Call + 136
    45  Python                              0x0000000106ff35e0 t_bootstrap + 71
    46  Python                              0x0000000106fba192 pythread_wrapper + 25
    47  libsystem_pthread.dylib             0x00007fff7f2132eb _pthread_body + 126
    48  libsystem_pthread.dylib             0x00007fff7f216249 _pthread_start + 66
    49  libsystem_pthread.dylib             0x00007fff7f21240d thread_start + 13
)
libc++abi.dylib: terminating with uncaught exception of type NSException
Abort trap: 6

[LysSanzMoreta]

@MooersLab So sorry for some reason I did not see this issue until now. It is probably too late but anyways, might be helpful to others.

I am not sure what did you mean about PyMol issues (keep in mind that then it would be a PyMOL issue, not mine). If it is helpful, I think I was using PyMOL 2.3.4 on Ubuntu 20.04. I can at some point try making the script work with an updated PyMOL version. However, note that calling the GUI from PyMOL from a script is a not very stable feature from PyMOl and in later projects I also struggled with it.