VMD-L Mailing List

From: Stipe Mustać (stipe.mustac_at_pharma.unizg.hr)
Date: Tue Jan 28 2025 - 08:10:58 CST

I downloaded the updated code and now the vmd-python seems to work. I
still get the error message "Pyright: "molecule" is unknown import
symbol" (and same for any member of vmd module) in the line with "from
vmd import molecule" but I guess I should not bother with that error and
now everything runs as it is supposed to?

Thank you very much once again for your assistance!

Best,
Stipe

On 1/28/25 9:18 AM, Stipe Mustać wrote:
>  Hi Robin,
>
> How do you mean „it is unlikely to fix compilation error“? I am not
> sure if we understood eachother completely. I am able to compile
> „regular“ vmd, if by „regular“ you mean on version downloadable from
> the official site, using python 3.13 and with minor changes Josh
> previously suggested.
>
> Best,
> Stipe
>
>> Am 28.01.2025 um 08:47 schrieb Robin Betz <robin_at_robinbetz.com>:
>>
>> 
>> Hi Stipe,
>>
>> This code defines a new python type, atomsel, by instantiating the
>> PyTypeObject struct directly. The fields in that struct change with
>> every minor version, and there were changes in Python 3.11 and 3.12
>> afaik, so copying the file from the repo is unlikely to fix the
>> compilation errors you're seeing.
>>
>> I updated vmd-python to use the more future-proof way of
>> instantiating the type from a specification object, but it required
>> some changes to other files. I'll see if I can get a patch up for
>> "regular" VMD to do this in the next few days, or you can look at the
>> vmd-python repo for this commit that should mostly apply:
>> https://urldefense.com/v3/__https://github.com/Eigenstate/vmd-python/commit/7753e8cd7bc6574540ae63d8272f5b732b823317__;!!DZ3fjg!9aVwSQk6IaYbGO_snNPy-2E9m6uKF_xAnvjwsViLVT0kPp-Ekyt2kneHCn4Xf9_is-Ywzt5THO2eggLWFtY44B2FvzcV8KY$
>>
>> Bset,
>> Robin
>>
>> On Mon, Jan 27, 2025 at 3:09 AM Stipe Mustać
>> <stipe.mustac_at_pharma.unizg.hr> wrote:
>>
>> Hi Robin,
>>
>> First of all I want to apologize for answering a bit later, I was
>> really away for the weekend. I really didn't expect to get the
>> answer from the creator himself, thank you very much for finding
>> some time to answer.
>>
>> When I use tcl interpreter i am also able to write some tcl
>> scripts which I can after that use inside the vmd to manipulate
>> my system (writing script and then sourcing with vmd tcl
>> interpreter). I believe in some cases that i also used some
>> features or packages which weren't inherently built into vmd.
>> Can't I do the same with python interpreter? I mean write some
>> script which uses some other python package (e.g. numpy) and run
>> that script using vmd python interpreter?
>>
>> As for the error, I knew I had to change the same things as I did
>> with regular build. But some parts of code still aren't the same
>> which causes new errors to arise. I will open up an issue on
>> github, but despite of that i will also write it here once again
>> in case someone with the same issue looking here for the answer
>> finds it.
>>
>> ---error:---
>>
>> py_atomsel.C:2138:24: error: invalid conversion from
>> ‘PyTypeObject*’ {aka ‘_typeobject*’} to ‘Py_ssize_t’ {aka ‘long
>> int’} [-fpermissive]
>>  2138 |     PyObject_HEAD_INIT(&PyType_Type)
>> /usr/include/python3.13/object.h:138:10: note: in definition of
>> macro ‘PyObject_HEAD_INIT’
>>   138 |         (type)                      \
>>       |          ^~~~
>> In file included from PluginMgr.h:31,
>>                  from VMDApp.h:23,
>>                  from py_atomsel.C:21:
>> ResizeArray.h: In instantiation of ‘void
>> ResizeArray<T>::append(const T&) [with T = Matrix4]’:
>> BaseMolecule.h:460:55:   required from here
>>   460 |   void add_instance(Matrix4 & inst) {
>> instances.append(inst); }
>>       | ~~~~~~~~~~~~~~~~^~~~~~
>> ResizeArray.h:108:13: warning: ‘void* memcpy(void*, const void*,
>> size_t)’ writing to an object of type ‘class Matrix4’ with no
>> trivial copy-assignment; use copy-assignment or
>> copy-initialization instead [-Wclass-memaccess]
>>   108 |       memcpy(newdata, data, currSize * sizeof(T));
>>       | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>> In file included from Timestep.h:29,
>>                  from BaseMolecule.h:36,
>>                  from DrawMolecule.h:26,
>>                  from Molecule.h:27,
>>                  from MoleculeList.h:26,
>>                  from py_atomsel.C:22:
>> Matrix4.h:26:7: note: ‘class Matrix4’ declared here
>>    26 | class Matrix4 {
>>       |       ^~~~~~~
>> make: *** [Makefile:536: py_atomsel.o] Error 1
>> Traceback (most recent call last):
>>
>> ---code downloaded from your website:---
>>
>> #if PY_MAJOR_VERSION >= 3
>>   PyTypeObject itertype = {
>>     PyObject_HEAD_INIT(&PyType_Type)
>>     "atomsel.iterator",
>>     sizeof(atomsel_iterobject), 0, // basic, item size
>>     (destructor)iter_dealloc, // dealloc
>>     0, //tp_print
>>     0, 0, // tp get and setattr
>>     0, // tp_as_async
>>     0, // tp_repr
>>     0, 0, 0, // as number, sequence, mapping
>>     0, 0, 0, // hash, call, str
>>     PyObject_GenericGetAttr, 0, // getattro, setattro
>>     0, // tp_as_buffer
>>     Py_TPFLAGS_DEFAULT, // flags
>>     0, // docstring
>>     0, 0, 0, // traverse, clear, richcompare
>>     0, // tp_weaklistoffset
>>     PyObject_SelfIter, // tp_iter
>>     (iternextfunc)iter_next, // tp_iternext
>>     iter_methods, // tp_methods
>>     0, 0, 0, // members, getset, base
>> };
>>
>> PyTypeObject Atomsel_Type = {
>>     PyObject_HEAD_INIT(0)
>>     "atomsel",
>>     sizeof(PyAtomSelObject), 0, // basic, item size
>>     (destructor)atomsel_dealloc, //dealloc
>>     0, // tp_print
>>     0, 0, // tp get and set attr
>>     0, // tp_as_async
>>     (reprfunc)atomsel_repr, // tp_repr
>>     0, 0, &atomsel_mapping, // as number, sequence, mapping
>>     0, 0, (reprfunc)atomsel_str, // hash, call, str
>>     (getattrofunc) atomsel_getattro, // getattro
>>     (setattrofunc) atomsel_setattro, // setattro
>>     0, // tp_as_buffer
>>     Py_TPFLAGS_DEFAULT|Py_TPFLAGS_BASETYPE, // flags
>>     atomsel_doc, // docstring
>>     0, 0, 0, // traverse, clear, richcompare
>>     0, // tp_weaklistoffset
>>     atomsel_iter, // tp_iter
>>     0, // tp_iternext
>>     atomselection_methods, // tp_methods,
>>     0, atomsel_getset, 0, // members, getset, base
>>     0, 0, 0, // tp_dict, descr_get, descr_set
>>     0, 0, // dictoffset, init
>>     PyType_GenericAlloc, // tp_alloc
>>     atomsel_new, // tp_new
>>     PyObject_Del, // tp_free
>> };
>>
>> ---source code downloaded from the official site:---
>>
>> #if PY_MAJOR_VERSION >= 3
>>   PyTypeObject itertype = {
>>     // XXX Clang++ doesn't like this initializer, see PEP 3123:
>>     // https://urldefense.com/v3/__https://www.python.org/dev/peps/pep-3123/__;!!DZ3fjg!9aVwSQk6IaYbGO_snNPy-2E9m6uKF_xAnvjwsViLVT0kPp-Ekyt2kneHCn4Xf9_is-Ywzt5THO2eggLWFtY44B2FnIJS_6A$
>>     //     See also:
>>     //
>> https://urldefense.com/v3/__http://python3porting.com/cextensions.html*module-initialization__;Iw!!DZ3fjg!9aVwSQk6IaYbGO_snNPy-2E9m6uKF_xAnvjwsViLVT0kPp-Ekyt2kneHCn4Xf9_is-Ywzt5THO2eggLWFtY44B2FF9vN6S0$
>>     // https://urldefense.com/v3/__https://docs.python.org/3.7/extending/newtypes.html__;!!DZ3fjg!9aVwSQk6IaYbGO_snNPy-2E9m6uKF_xAnvjwsViLVT0kPp-Ekyt2kneHCn4Xf9_is-Ywzt5THO2eggLWFtY44B2FdsTlduo$
>>     // PyObject_HEAD_INIT(&PyType_Type)
>>     PyVarObject_HEAD_INIT(NULL, 0)
>>     "atomsel.iterator",
>>     sizeof(atomsel_iterobject), 0, // basic, item size
>>     (destructor)iter_dealloc, // dealloc
>>     0, //tp_print
>>     0, 0, // tp get and setattr
>>     0, // tp_as_async
>>     0, // tp_repr
>>     0, 0, 0, // as number, sequence, mapping
>>     0, 0, 0, // hash, call, str
>>     PyObject_GenericGetAttr, 0, // getattro, setattro
>>     0, // tp_as_buffer
>>     Py_TPFLAGS_DEFAULT, // flags
>>     0, // docstringHi Robin,
>>     0, 0, 0, // traverse, clear, richcompare
>>     0, // tp_weaklistoffset
>>     PyObject_SelfIter, // tp_iter
>>     (iternextfunc)iter_next, // tp_iternext
>>     iter_methods, // tp_methods
>>     0, 0, 0, // members, getset, base
>>   };
>>
>>   PyTypeObject Atomsel_Type = {
>>     // XXX Clang++ doesn't like this initializer:
>>     // https://urldefense.com/v3/__https://www.python.org/dev/peps/pep-3123/__;!!DZ3fjg!9aVwSQk6IaYbGO_snNPy-2E9m6uKF_xAnvjwsViLVT0kPp-Ekyt2kneHCn4Xf9_is-Ywzt5THO2eggLWFtY44B2FnIJS_6A$
>>     //     See also:
>>     //
>> https://urldefense.com/v3/__http://python3porting.com/cextensions.html*module-initialization__;Iw!!DZ3fjg!9aVwSQk6IaYbGO_snNPy-2E9m6uKF_xAnvjwsViLVT0kPp-Ekyt2kneHCn4Xf9_is-Ywzt5THO2eggLWFtY44B2FF9vN6S0$
>>     // https://urldefense.com/v3/__https://docs.python.org/3.7/extending/newtypes.html__;!!DZ3fjg!9aVwSQk6IaYbGO_snNPy-2E9m6uKF_xAnvjwsViLVT0kPp-Ekyt2kneHCn4Xf9_is-Ywzt5THO2eggLWFtY44B2FdsTlduo$
>>     // PyObject_HEAD_INIT(0)
>>     PyVarObject_HEAD_INIT(NULL, 0)
>>     "atomsel",
>>     sizeof(PyAtomSelObject), 0, // basic, item size
>>     (destructor)atomsel_dealloc, //dealloc
>>     0, // tp_print
>>     0, 0, // tp get and set attr
>>     0, // tp_as_async
>>     (reprfunc)atomsel_repr, // tp_repr
>>     0, 0, &atomsel_mapping, // as number, sequence, mapping
>>     0, 0, (reprfunc)atomsel_str, // hash, call, str
>>     (getattrofunc) atomsel_getattro, // getattro
>>     (setattrofunc) atomsel_setattro, // setattro
>>     0, // tp_as_buffer
>>     Py_TPFLAGS_DEFAULT|Py_TPFLAGS_BASETYPE, // flags
>>     atomsel_doc, // docstring
>>     0, 0, 0, // traverse, clear, richcompare
>>     0, // tp_weaklistoffset
>>     atomsel_iter, // tp_iter
>>     0, // tp_iternext
>>     atomselection_methods, // tp_methods,
>>     0, atomsel_getset, 0, // members, getset, base
>>     0, 0, 0, // tp_dict, descr_get, descr_set
>>     0, 0, // dictoffset, init
>>     PyType_GenericAlloc, // tp_alloc
>>     atomsel_new, // tp_new
>>     PyObject_Del, // tp_free
>>   };
>>
>> Is it safe to replace this code chunk by the official one to
>> solve this error?
>>
>> Best,
>> Stipe
>>
>> On 1/23/25 5:33 AM, Robin Betz wrote:
>>> Hi Stipe,
>>>
>>> vmd-python is an importable Python module that is used from
>>> other scripts that run in the Python interpreter. It's useful
>>> for running analyses, etc, using Python scripts that may use
>>> other packages, and doesn't have the visualization window.
>>> "Regular" VMD is a standalone executable that embeds an
>>> interpreter (either Python or TCL) that can be used to interact
>>> with the program. I use "regular" VMD for visualizing and
>>> exploring MD systems and trajectories, and then write scripts
>>> that use vmd-python to perform analyses and generate plots.
>>>
>>> You'll get the same compilation errors you had for Python 3.13 +
>>> VMD trying to build vmd-python. If you open up an issue on the
>>> github (https://urldefense.com/v3/__https://github.com/Eigenstate/vmd-python__;!!DZ3fjg!9aVwSQk6IaYbGO_snNPy-2E9m6uKF_xAnvjwsViLVT0kPp-Ekyt2kneHCn4Xf9_is-Ywzt5THO2eggLWFtY44B2Fnmig9LU$
>>> <https://urldefense.com/v3/__https://github.com/Eigenstate/vmd-python__;!!DZ3fjg!5l7DtkIA3Lqg2MdXtD8UY3aLIy28zM-7rOJ848KJ80dXS_OJK0A15h2_C0NIVhN-chZtPN9sR-23dBJ9UA$>)
>>> I'll try to get to it. There's conda builds available but only
>>> through Python 3.1-- that's also something I've been meaning to fix.
>>>
>>> Best,
>>> Robin
>>>
>>> On Wed, Jan 22, 2025 at 4:20 PM Stipe Mustać
>>> <stipe.mustac_at_pharma.unizg.hr> wrote:
>>>
>>> Dear Josh,
>>>
>>> Thanks for your help (and after some additional struggles) I
>>> finally managed to compile the vmd with python interpreter.
>>> I didn't install any programs listed in the documentation as
>>> dependencies (surf, stride, tachyon) but the software seems
>>> to run normally?
>>>
>>> I tried to compile vmd-python by Robin Betz, but i have some
>>> other compilation errors too which for now I can't solve.
>>> Should I open a new topic or can I go on here with that
>>> compilation error here? I also don't understand what are the
>>> advantages of vmd-python over just using vmd with python
>>> interpreter regularly?
>>>
>>> Thank you very much once again, I would never be able to
>>> solve this struggle without your assistance.
>>> Sincerely,
>>> Stipe
>>>
>>> On 1/21/25 8:04 PM, Josh Vermaas wrote:
>>>> Hi Stipe,
>>>>
>>>> Lets try to keep this in VMD-L, so that future googlers can
>>>> figure out what the problem was. I think this is more of
>>>> the same. Looks like you are using python 3.13, while my
>>>> Ubuntu machine uses 3.12. The key line from your logs are
>>>> these:
>>>>
>>>> PythonTextInterp.C:105:24: error: ‘PyEval_CallObject’ was
>>>> not declared in this scope; did you mean ‘PyObject_CallObject’?
>>>> PythonTextInterp.C:177:3: error: ‘PySys_AddWarnOption’ was
>>>> not declared in this scope; did you mean
>>>> ‘PySys_ResetWarnOptions’?
>>>>
>>>> For what I am sure are good reasons, occasionally python
>>>> deprecates parts of their API. In this case, VMD is
>>>> depending on PyEval_CallObject and PySys_AddWarnOption.
>>>> PyEval_CallObject was deprecated in 3.9, and was removed as
>>>> of 3.13, which is why you are running into issues compiling
>>>> it. Based on a bit of googling, it looks like you just use
>>>> PyObject_CallObject instead.
>>>>
>>>> For AddWarnOption it looks like the API changed pretty
>>>> drastically. I'm not actually sure what happens if we have
>>>> no warn options, so you may want to consider just exempting
>>>> python 3.13 and higher from AddWarnOption, as we just add
>>>> the defaults anyway. So something like this:
>>>>
>>>> #if PY_MAJOR_VERSION >= 3 && PY_MINOR_VERSION <= 12
>>>>   PySys_AddWarnOption(L"default");
>>>> #elif PY_MAJOR_VERSION < 3
>>>>   PySys_AddWarnOption((char*) "default");
>>>> #endif
>>>>
>>>> I know Diego has been working quite a bit on a "VMD 2.0"
>>>> that hopefully has all these deprecations taken care of.
>>>>
>>>> -Josh
>>>>
>>>>
>>>> On 1/21/25 12:39 PM, Stipe Mustać wrote:
>>>>>
>>>>> Hi Josh,
>>>>>
>>>>> I changed the mentioned lines and the compilation finished
>>>>> without reporting any errors. Then I went on to compile
>>>>> vmd, and got the following:
>>>>>
>>>>> Compiling  PythonTextInterp.C -->  PythonTextInterp.o  ...
>>>>> PythonTextInterp.C: In function ‘void call_callbacks(const
>>>>> char*, PyObject*)’:
>>>>> PythonTextInterp.C:105:24: error: ‘PyEval_CallObject’ was
>>>>> not declared in this scope; did you mean
>>>>> ‘PyObject_CallObject’?
>>>>>   105 |     PyObject *result = PyEval_CallObject(obj,
>>>>> arglist);
>>>>>       | ^~~~~~~~~~~~~~~~~
>>>>>       | PyObject_CallObject
>>>>> PythonTextInterp.C: In constructor
>>>>> ‘PythonTextInterp::PythonTextInterp(VMDApp*)’:
>>>>> PythonTextInterp.C:177:3: error: ‘PySys_AddWarnOption’ was
>>>>> not declared in this scope; did you mean
>>>>> ‘PySys_ResetWarnOptions’?
>>>>>   177 | PySys_AddWarnOption(L"default");
>>>>>       |   ^~~~~~~~~~~~~~~~~~~
>>>>>       |   PySys_ResetWarnOptions
>>>>> PythonTextInterp.C:199:16: warning: ‘void
>>>>> PySys_SetArgv(int, wchar_t**)’ is deprecated
>>>>> [-Wdeprecated-declarations]
>>>>>   199 |   PySys_SetArgv(argc, wargv);
>>>>>       |   ~~~~~~~~~~~~~^~~~~~~~~~~~~
>>>>> In file included from /usr/include/python3.13/Python.h:125,
>>>>>                  from py_commands.h:24,
>>>>>                  from PythonTextInterp.C:21:
>>>>> /usr/include/python3.13/sysmodule.h:10:38: note: declared here
>>>>>    10 | Py_DEPRECATED(3.11) PyAPI_FUNC(void)
>>>>> PySys_SetArgv(int, wchar_t **);
>>>>> | ^~~~~~~~~~~~~
>>>>> make: *** [Makefile:621: PythonTextInterp.o] Error 1
>>>>>
>>>>> I am not sure if i provided the right directories as
>>>>> libraries or is it really some python syntax problem? Log
>>>>> file again in attachment.
>>>>>
>>>>> Thank you very much once again for your assistance.
>>>>>
>>>>> Stipe
>>>>>
>>>>> On 1/21/25 5:53 PM, Josh Vermaas wrote:
>>>>>> Hi Stipe,
>>>>>>
>>>>>> Based on the log you attached, you want to look for
>>>>>> compiler errors. I see this in the log you attached:
>>>>>>
>>>>>> src/qcschemaplugin.c: In function ‘open_qcschema_read’:
>>>>>> src/qcschemaplugin.c:162:29: error: assignment to ‘int’
>>>>>> from ‘struct _json_value *’ makes integer from pointer
>>>>>> without a cast [-Wint-conversion]
>>>>>>   162 |           data->totalcharge =
>>>>>> aux_value->u.object.values[j].value;
>>>>>>       |                             ^
>>>>>> src/qcschemaplugin.c:165:30: error: assignment to ‘int’
>>>>>> from ‘struct _json_value *’ makes integer from pointer
>>>>>> without a cast [-Wint-conversion]
>>>>>>   165 | data->multiplicity =
>>>>>> aux_value->u.object.values[j].value;
>>>>>>
>>>>>> To me, this looks like your compiler is pickier than
>>>>>> mine, and is treating something that used to be a warning
>>>>>> into a full-blown error. See
>>>>>> https://urldefense.com/v3/__https://gcc.gnu.org/bugzilla/show_bug.cgi?id=106416__;!!DZ3fjg!9aVwSQk6IaYbGO_snNPy-2E9m6uKF_xAnvjwsViLVT0kPp-Ekyt2kneHCn4Xf9_is-Ywzt5THO2eggLWFtY44B2FpozMJCE$
>>>>>> <https://urldefense.com/v3/__https://gcc.gnu.org/bugzilla/show_bug.cgi?id=106416__;!!HXCxUKc!0gXBBlCKD1JmI3G9yQRw9h2LyV4GBDdHs2sBsXyx7GpOMLrJpvzrRPhrE04oA2ru5H0Y-ZlIirL-qdqS7TgRr7NCaBz5NQ$>
>>>>>> which makes this look like the intended behavior
>>>>>> nowadays, which is unfortunate since this particular
>>>>>> plugin hasn't been changed in YEARS. I think you could
>>>>>> make the compiler happy by adding in the cast there:
>>>>>>
>>>>>> data->totalcharge = (int)
>>>>>> aux_value->u.object.values[j].value;
>>>>>> data->multiplicity = (int)
>>>>>> aux_value->u.object.values[j].value;
>>>>>>
>>>>>> Or alternatively changing the compiler flags to make that
>>>>>> error a warning again.
>>>>>>
>>>>>> -Josh
>>>>>>
>>>>>>
>>>>>> On 1/21/25 11:18 AM, Stipe Mustać wrote:
>>>>>>> Hello Josh!
>>>>>>>
>>>>>>> Thank you very much for the links you provided. I used
>>>>>>> them all and I can compile nothing. Neither vmd nor
>>>>>>> vmd-python. I actually realized later i have to compile
>>>>>>> vmd from source and that is what i am trying to do the
>>>>>>> entire day today. I was mostly referring to the guide
>>>>>>> posted by Robin Betz. Unfortunately I can‘t even compile
>>>>>>> the plugins. The error I get when compiling plugins is:
>>>>>>>
>>>>>>> make[2]: *** [Makefile:556:
>>>>>>> ../compile/lib_LINUXAMD64/molfile/qcschemaplugin.o] Error 1
>>>>>>> make[2]: Leaving directory
>>>>>>> '/home/stipe/downloads/vmdpackaging/plugins/molfile_plugin'
>>>>>>> make[1]: *** [Makefile:164: molfilelibs] Error 1
>>>>>>> make[1]: Leaving directory
>>>>>>> '/home/stipe/downloads/vmdpackaging/plugins'
>>>>>>> make: *** [Make-arch:338: LINUXAMD64] Error 2
>>>>>>>
>>>>>>> I applied that sed command you provided in your guide to
>>>>>>> switch from tcl 8.5 to 8.6. I am sending the entire make
>>>>>>> output in the attachment. I haven’t still installed
>>>>>>> surf, stride or tachyon. My os is arch linux and it uses
>>>>>>> python 3.13.
>>>>>>>
>>>>>>> Thank you once again.
>>>>>>> Sincerely,
>>>>>>> Stipe Mustac
>>>>>>>
>>>>>>>
>>>>>>> > Am 21.01.2025 um 16:23 schrieb Josh Vermaas
>>>>>>> <vermaasj_at_msu.edu> <mailto:vermaasj_at_msu.edu>:
>>>>>>> >
>>>>>>> > Hi Stipe,
>>>>>>> >
>>>>>>> > How did you install VMD? The default VMD installations
>>>>>>> that you can download from the ks.uiuc.edu
>>>>>>> <http://ks.uiuc.edu> website don't come with a python
>>>>>>> interpreter built-in. Instead, if you want python and
>>>>>>> graphics, you end up needing to compile VMD yourself.
>>>>>>> https://urldefense.com/v3/__https://robinbetz.com/blog/2015/01/08/compiling-vmd-with-python-support/__;!!DZ3fjg!5Cp0UHc8gqyWY_z16AWli_FiYQKIyw3BouVGyNUkt9XAZL4zSZdjwo-vEOH5HAHnuSGU33rJAEKLeSGKjP8$
>>>>>>> has a blogpost describing the process, and she's also
>>>>>>> got a way of installing VMD as a python package
>>>>>>> (https://urldefense.com/v3/__https://vmd.robinbetz.com/__;!!DZ3fjg!5Cp0UHc8gqyWY_z16AWli_FiYQKIyw3BouVGyNUkt9XAZL4zSZdjwo-vEOH5HAHnuSGU33rJAEKLw_8HEtI$
>>>>>>> ). I've got packaging instructions for alpha versions of
>>>>>>> VMD that I use within my lab as well.
>>>>>>> https://urldefense.com/v3/__https://github.com/jvermaas/vmd-packaging-instructions__;!!DZ3fjg!5Cp0UHc8gqyWY_z16AWli_FiYQKIyw3BouVGyNUkt9XAZL4zSZdjwo-vEOH5HAHnuSGU33rJAEKL8qbMb2s$
>>>>>>> > Hope this helps!
>>>>>>> >
>>>>>>> > -Josh
>>>>>>> >
>>>>>>> >
>>>>>>> >> On 1/20/25 2:18 PM, Stipe Mustać wrote:
>>>>>>> >> Hello! I am trying to use python interpreter in vmd.
>>>>>>> The error message I keep getting is:
>>>>>>> >>
>>>>>>> >> Info) Starting Python...
>>>>>>> >> 'import site' failed; use -v for traceback
>>>>>>> >> rlwrap: warning: vmd crashed, killed by SIGSEGV (core
>>>>>>> dumped).
>>>>>>> >> rlwrap itself has not crashed, but for transparency,
>>>>>>> >> it will now kill itself with the same signal
>>>>>>> >>
>>>>>>> >> warnings can be silenced by the --no-warnings (-n) option
>>>>>>> >> Segmentation fault (core dumped)
>>>>>>> >>
>>>>>>> >> I saw a person who posted in this mailing list having
>>>>>>> the same issue in 2023, tried to reproduce all the
>>>>>>> tutorials and guides, but without any success. I would
>>>>>>> appreciate any help.
>>>>>>> >>
>>>>>>> >> Sincerely,
>>>>>>> >> Stipe Mustac
>>>>>>> >>
>>>>>>> >
>>>>>>> > --
>>>>>>> > Josh Vermaas
>>>>>>> >
>>>>>>> > vermaasj_at_msu.edu
>>>>>>> > Assistant Professor, Plant Research Laboratory and
>>>>>>> Biochemistry and Molecular Biology
>>>>>>> > Michigan State University
>>>>>>> > vermaaslab.github.io
>>>>>>> <https://urldefense.com/v3/__http://vermaaslab.github.io__;!!DZ3fjg!5l7DtkIA3Lqg2MdXtD8UY3aLIy28zM-7rOJ848KJ80dXS_OJK0A15h2_C0NIVhN-chZtPN9sR-3j4Yzeaw$>
>>>>>>> >
>>>>>>> >
>>>>>>
>>>>>> --
>>>>>> Josh Vermaas
>>>>>>
>>>>>> vermaasj_at_msu.edu
>>>>>> Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
>>>>>> Michigan State University
>>>>>> vermaaslab.github.io <https://urldefense.com/v3/__http://vermaaslab.github.io__;!!DZ3fjg!5l7DtkIA3Lqg2MdXtD8UY3aLIy28zM-7rOJ848KJ80dXS_OJK0A15h2_C0NIVhN-chZtPN9sR-3j4Yzeaw$>
>>>>
>>>> --
>>>> Josh Vermaas
>>>>
>>>> vermaasj_at_msu.edu
>>>> Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
>>>> Michigan State University
>>>> vermaaslab.github.io <https://urldefense.com/v3/__http://vermaaslab.github.io__;!!DZ3fjg!5l7DtkIA3Lqg2MdXtD8UY3aLIy28zM-7rOJ848KJ80dXS_OJK0A15h2_C0NIVhN-chZtPN9sR-3j4Yzeaw$>
>>>