Yes, it seems that this is exactly the problem. I'm using PyMOL 1.3, and
the Python version it is using is 2.5.4...
Is there any way of fixing it without uninstalling my current version of
PyMOL?
2016-01-29 11:57 GMT-02:00 Matthew Baumgartner <mp...@pitt.edu>:
> What version of Pymol are you using? Pymol ships with it's own version of
> python that is separate from your system python.
> In the pymol command line, run:
>
> import sys
> print sys.version
>
> That will tell you what python version pymol is using.
>
> HTH,
> Matt
>
>
> On 01/29/2016 08:55 AM, Guilherme Souza wrote:
>
> I've searched about this kind of error, and in every site I look, it seems
> that it is caused by using Python <= 2.5, which is not my case. Is there
> any chance that my PyMOL is using and older version of Python?
>
> 2016-01-29 11:46 GMT-02:00 Guilherme Souza <gsouza...@gmail.com>:
>
>> Okay. I did it, and kind of got the same error:
>>
>> PyMOL>run colorbyrmsd.py
>> Traceback (most recent call last):
>> File "C:\Program Files (x86)\PyMOL\PyMOL/modules\pymol\parser.py", line
>> 338, in parse
>> parsing.run_file(path,self.pymol_names,self.pymol_names)
>> File "C:\Program Files (x86)\PyMOL\PyMOL/modules\pymol\parsing.py",
>> line 455, in run_file
>> execfile(file,global_ns,local_ns)
>> SyntaxError: future feature print_function is not defined
>> (colorbyrmsd.py, line 10)
>>
>> 2016-01-29 11:41 GMT-02:00 Matthew Baumgartner < <mp...@pitt.edu>
>> mp...@pitt.edu>:
>>
>>> Hi,
>>> You run the command 'run colorbyrmsd.py' in the Pymol command line. That
>>> initializes the function in pymol. If everything goes well, you shouldn't
>>> see anything (no errors). Then to use the command, type just 'colorbyrmsd
>>> [args...]' into the command line.
>>>
>>> You can see the usage instructions in the wiki.
>>>
>>> HTH,
>>>
>>> Matt Baumgartner
>>>
>>>
>>> On 01/29/2016 08:36 AM, Guilherme Souza wrote:
>>>
>>> I'm sorry.. Where exactly am I supposed to type 'run colorbyrmsd.py'?
>>> And should I expect to see my both protein structures colored in the
>>> PyMOL interface?
>>>
>>> Thank you!
>>>
>>> 2016-01-29 11:36 GMT-02:00 Guilherme Souza < <gsouza...@gmail.com>
>>> gsouza...@gmail.com>:
>>>
>>>> I'm sorry.. Where exactly am I supposed to type 'run colorbyrmsd.py'?
>>>> And should I expect to see my both protein structures colored in the
>>>> PyMOL interface?
>>>>
>>>> 2016-01-29 11:35 GMT-02:00 Guilherme Souza < <gsouza...@gmail.com>
>>>> gsouza...@gmail.com>:
>>>>
>>>>> I'm sorry.. Where exactly am I supposed to type 'run colorbyrmsd.py'?
>>>>> And should I expect to see my both protein structures colored in the
>>>>> PyMOL interface?
>>>>>
>>>>> Thank you!
>>>>>
>>>>> 2016-01-29 11:09 GMT-02:00 Schubert, Carsten [JRDUS] <
>>>>> <cschu...@its.jnj.com>cschu...@its.jnj.com>:
>>>>>
>>>>>> Hi Guilherme,
>>>>>>
>>>>>>
>>>>>>
>>>>>> the script is not a plugin, so you cannot install it since it is
>>>>>> missing some software infrastructure to work as a plugin. Simply put the
>>>>>> script into the directory you are working in and run it via ‘run
>>>>>> colorbyrmsd.py’ . This will add the command to the scripting interface
>>>>>> and
>>>>>> you can run the command like any other pymol command. See the wiki for
>>>>>> the
>>>>>> details in that regards.
>>>>>>
>>>>>>
>>>>>>
>>>>>> HTH
>>>>>>
>>>>>>
>>>>>>
>>>>>> Carsten
>>>>>>
>>>>>>
>>>>>>
>>>>>> *From:* Guilherme Souza [mailto: <gsouza...@gmail.com>
>>>>>> gsouza...@gmail.com]
>>>>>> *Sent:* Friday, January 29, 2016 7:07 AM
>>>>>> *To:* <pymol-users@lists.sourceforge.net>
>>>>>> pymol-users@lists.sourceforge.net
>>>>>> *Subject:* [PyMOL] ColorByRMSD script
>>>>>>
>>>>>>
>>>>>>
>>>>>> Hi.
>>>>>>
>>>>>>
>>>>>>
>>>>>> I'm a starter in PyMOL, and I'm trying to use this script,
>>>>>> ColorByRMSD ( <http://www.pymolwiki.org/index.php/ColorByRMSD>
>>>>>> http://www.pymolwiki.org/index.php/ColorByRMSD). However, I'm
>>>>>> getting the following error message, when I initialize PyMOL after
>>>>>> installing the plugin:
>>>>>>
>>>>>>
>>>>>>
>>>>>> Exception in plugin 'colorbyrmsd' -- Traceback follows...
>>>>>>
>>>>>> Traceback (most recent call last):
>>>>>>
>>>>>> File "C:\Program Files (x86)\PyMOL\PyMOL/modules\pmg_tk\PMGApp.py",
>>>>>> line 313, in initializePlugins
>>>>>>
>>>>>> __builtin__.__import__(mod_name)
>>>>>>
>>>>>> SyntaxError: future feature print_function is not defined
>>>>>> (colorbyrmsd.py, line 10)
>>>>>>
>>>>>> Error: unable to initialize plugin 'colorbyrmsd'.
>>>>>>
>>>>>>
>>>>>>
>>>>>> I'm using Python 2.7, and I've already checked '__future__' module,
>>>>>> and 'print_function' is there, so I don't know what could be causing
>>>>>> this.
>>>>>>
>>>>>>
>>>>>>
>>>>>> I'd be glad if anyone could give me a help.
>>>>>>
>>>>>>
>>>>>>
>>>>>> Thank you.
>>>>>>
>>>>>
>>>>>
>>>>
>>>
>>>
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>>
>>
>
>
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