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
<mailto: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
<mailto: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 <mailto: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 <mailto: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 <mailto: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
<mailto:gsouza...@gmail.com>]
*Sent:* Friday, January 29, 2016 7:07 AM
*To:* pymol-users@lists.sourceforge.net
<mailto: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).
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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