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
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
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 :
> I'm sorry.. Where exactly am I supposed to type 'run colorbyrmsd.py'?
> And should I expect to
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 :
> I'm sorry.. Where exactly am I supposed to type 'run colorbyrmsd.py'?
> And should
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
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\PyMO
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 :
> Okay. I did it, and kind of got the sam
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 wrot
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 :
> What version of Pymol are you using? Pymol ships w
Hi Guilherme,
Simply remove the __future__ import line from the script. The script will work
just fine in PyMOL 1.3.
Cheers,
Thomas
On 29 Jan 2016, at 09:00, Guilherme Souza wrote:
> Yes, it seems that this is exactly the problem. I'm using PyMOL 1.3, and the
> Python version it is using i
Thank you so much!
Worked perfectly fine.
2016-01-29 13:08 GMT-02:00 Thomas Holder :
> Hi Guilherme,
>
> Simply remove the __future__ import line from the script. The script will
> work just fine in PyMOL 1.3.
>
> Cheers,
> Thomas
>
> On 29 Jan 2016, at 09:00, Guilherme Souza wrote:
>
> > Yes
I am trying to show some cell surface receptors and to indicate their position
relative to the membrane.
I thought to indicate the plane of the membrane by a flat disk, a ago cylinder.
x1,y1,z1 = 0, -1, 0 # start point
r1,g1,b1 = 1, 1, 0 # color (yellow)
x2,y2,z2 = 0, -2, 0 # end point
r2,g2,b2
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