pymol-users Mailing List for PyMOL Molecular Graphics System

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 = 1, 1, 0 # color (yellow)
radius = 100
cmd.load_cgo( [ 9.0, x1, y1, z1, x2, y2, z2, radius, r1, g1, b1, r2, g2, b2 ], "membrane" )

When I try to move this cylinder into the correct position with cmd.transform_selection,
using the transformation parameters extracted from get_view (reordering them as needed)
I get the error message "Selector-Error: Invalid selection name “membrane” “

The same transform command works fine if I apply it to a pseudo atom originally generated with coordinates 0,0,0.

Any suggestion how else I could indicate the membrane, or how I could place my ego object parallel 
to the screen yz plane? I have to be able to do this in a reproducible fashion, as I have to  do this
for a large number of constructs that bend my receptors relative to the membrane in various ways. 

Thanks for your help
		Annemarie
	
_______________________________

Dr. Annemarie Honegger PhD
Department 
of Biochemistry
Zürich University
Winterthurerstrasse 190
CH-8057 Zürich
Switzerland

Thank you so much!

Worked perfectly fine.

2016-01-29 13:08 GMT-02:00 Thomas Holder <tho...@sc...>:

> 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 <gso...@gm...> wrote:
>
> > 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...@pi...>:
> > 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 <gso...@gm...>:
> >> 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...@pi...>:
> >> 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 <gso...@gm...>:
> >>> 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 <gso...@gm...>:
> >>> 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] <
> CSC...@it...>:
> >>> 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:gso...@gm...]
> >>> Sent: Friday, January 29, 2016 7:07 AM
> >>> To: pym...@li...
> >>> 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.
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

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 <gso...@gm...> wrote:

> 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...@pi...>:
> 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 <gso...@gm...>:
>> 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...@pi...>:
>> 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 <gso...@gm...>:
>>> 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 <gso...@gm...>:
>>> 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] <CSC...@it...>:
>>> 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:gso...@gm...] 
>>> Sent: Friday, January 29, 2016 7:07 AM
>>> To: pym...@li...
>>> 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.

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

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...@pi...>:

> 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 <gso...@gm...>:
>
>> 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...@pi...>
>> mp...@pi...>:
>>
>>> 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 < <gso...@gm...>
>>> gso...@gm...>:
>>>
>>>> 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 < <gso...@gm...>
>>>> gso...@gm...>:
>>>>
>>>>> 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] <
>>>>> <CSC...@it...>CSC...@it...>:
>>>>>
>>>>>> 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: <gso...@gm...>
>>>>>> gso...@gm...]
>>>>>> *Sent:* Friday, January 29, 2016 7:07 AM
>>>>>> *To:* <pym...@li...>
>>>>>> pym...@li...
>>>>>> *Subject:* [PyMOL] ColorByRMSD script
>>>>>>
>>>>>>
>>>>>>
>>>>>> Hi.
>>>>>>
>>>>>>
>>>>>>
>>>>>> I'm a starter in PyMOL, and I'm trying to use this script,
>>>>>> ColorByRMSD ( <" rel="nofollow">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.
>>>>>>
>>>>>
>>>>>
>>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>> Monitor end-to-end web transactions and take corrective actions now
>>> Troubleshoot faster and improve end-user experience. Signup Now!http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>
>>>
>>>
>>> _______________________________________________
>>> PyMOL-users mailing list (PyM...@li...)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pym...@li...
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>> Monitor end-to-end web transactions and take corrective actions now
>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>> _______________________________________________
>>> PyMOL-users mailing list ( <PyM...@li...>
>>> PyM...@li...)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pym...@li...
>>>
>>
>>
>
>

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 <gso...@gm... 
> <mailto:gso...@gm...>>:
>
>     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...@pi...
>     <mailto:mp...@pi...>>:
>
>         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
>>         <gso...@gm... <mailto:gso...@gm...>>:
>>
>>             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
>>             <gso...@gm... <mailto:gso...@gm...>>:
>>
>>                 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]
>>                 <CSC...@it... <mailto:CSC...@it...>>:
>>
>>                     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:gso...@gm...
>>                     <mailto:gso...@gm...>]
>>                     *Sent:* Friday, January 29, 2016 7:07 AM
>>                     *To:* pym...@li...
>>                     <mailto:pym...@li...>
>>                     *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.
>>
>>
>>
>>
>>
>>
>>         ------------------------------------------------------------------------------
>>         Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>         APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>         Monitor end-to-end web transactions and take corrective actions now
>>         Troubleshoot faster and improve end-user experience. Signup Now!
>>         http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>
>>
>>         _______________________________________________
>>         PyMOL-users mailing list (PyM...@li...
>>         <mailto:PyM...@li...>)
>>         Info Page:https://lists.sourceforge.net/lists/listinfo/pymol-users
>>         Archives:http://www.mail-archive.com/pym...@li...
>
>
>         ------------------------------------------------------------------------------
>         Site24x7 APM Insight: Get Deep Visibility into Application
>         Performance
>         APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>         Monitor end-to-end web transactions and take corrective
>         actions now
>         Troubleshoot faster and improve end-user experience. Signup Now!
>         http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>         _______________________________________________
>         PyMOL-users mailing list (PyM...@li...
>         <mailto:PyM...@li...>)
>         Info Page:
>         https://lists.sourceforge.net/lists/listinfo/pymol-users
>         Archives:
>         http://www.mail-archive.com/pym...@li...
>
>
>

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 <gso...@gm...>:

> 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...@pi...>:
>
>> 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 <gso...@gm...>:
>>
>>> 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 < <gso...@gm...>
>>> gso...@gm...>:
>>>
>>>> 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] <
>>>> CSC...@it...>:
>>>>
>>>>> 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: <gso...@gm...>
>>>>> gso...@gm...]
>>>>> *Sent:* Friday, January 29, 2016 7:07 AM
>>>>> *To:* <pym...@li...>
>>>>> pym...@li...
>>>>> *Subject:* [PyMOL] ColorByRMSD script
>>>>>
>>>>>
>>>>>
>>>>> Hi.
>>>>>
>>>>>
>>>>>
>>>>> I'm a starter in PyMOL, and I'm trying to use this script, ColorByRMSD
>>>>> ( <" rel="nofollow">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.
>>>>>
>>>>
>>>>
>>>
>>
>>
>> ------------------------------------------------------------------------------
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
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>>
>>
>>
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> Monitor end-to-end web transactions and take corrective actions now
>> Troubleshoot faster and improve end-user experience. Signup Now!
>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
>

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...@pi...>:

> 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 <gso...@gm...>:
>
>> 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 < <gso...@gm...>
>> gso...@gm...>:
>>
>>> 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] <
>>> CSC...@it...>:
>>>
>>>> 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: <gso...@gm...>
>>>> gso...@gm...]
>>>> *Sent:* Friday, January 29, 2016 7:07 AM
>>>> *To:* <pym...@li...>
>>>> pym...@li...
>>>> *Subject:* [PyMOL] ColorByRMSD script
>>>>
>>>>
>>>>
>>>> Hi.
>>>>
>>>>
>>>>
>>>> I'm a starter in PyMOL, and I'm trying to use this script, ColorByRMSD (
>>>> <" rel="nofollow">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.
>>>>
>>>
>>>
>>
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
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>
>
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>
>
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

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 <gso...@gm... 
> <mailto:gso...@gm...>>:
>
>     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 <gso...@gm...
>     <mailto:gso...@gm...>>:
>
>         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]
>         <CSC...@it... <mailto:CSC...@it...>>:
>
>             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:gso...@gm...
>             <mailto:gso...@gm...>]
>             *Sent:* Friday, January 29, 2016 7:07 AM
>             *To:* pym...@li...
>             <mailto:pym...@li...>
>             *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.
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

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 <gso...@gm...>:

> 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 <gso...@gm...>:
>
>> 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] <
>> CSC...@it...>:
>>
>>> 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:gso...@gm...]
>>> *Sent:* Friday, January 29, 2016 7:07 AM
>>> *To:* pym...@li...
>>> *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.
>>>
>>
>>
>

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 <gso...@gm...>:

> 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] <CSC...@it...
> >:
>
>> 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:gso...@gm...]
>> *Sent:* Friday, January 29, 2016 7:07 AM
>> *To:* pym...@li...
>> *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.
>>
>
>

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:gso...@gm...]
Sent: Friday, January 29, 2016 7:07 AM
To: pym...@li...
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.

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.

Dear Thomas

Thank you very much!!

Best Regards
Priyan

On Fri, Jan 29, 2016 at 5:13 AM, Thomas Holder <
tho...@sc...> wrote:

> Hi Spencer & Priyan,
>
> I've updated the show_bumps script to work with multi-state objects.
> Please re-download.
>
> Cheers,
>   Thomas
>
> On 28 Jan 2016, at 06:15, Spencer Bliven <spe...@gm...> wrote:
>
> > You can automate generating the bump objects:
> >
> > split_states *,prefix=split_
> > for n in cmd.get_object_list("(split_*)"): show_bumps(n, "bump_"+n);
> >
> > However, unfortunately the bump cgo objects don't seem to be able to be
> combined into a multi-state object (e.g. with `for n in
> cmd.get_object_list("(split_*)"):
> cmd.create("bumps","bump_"+n,target_state=-1)`). Thus you might have to
> generate your movie using some python loops to enable/disable the bumps for
> each frame, if you want to automate it.
> >
> > -Spencer
> >
> > On Thu, Jan 28, 2016 at 11:25 AM, ccp4 pymol <ccp...@gm...>
> wrote:
> > Dear Spencer
> >
> > Thank you for the suggestion. Well, I actually wanted to do it as a part
> of making a movie, so would have liked some automation.
> >
> > Thank you.
> >
> > Best Regards
> > Priyan
> >
> > On Thu, Jan 28, 2016 at 2:39 PM, Spencer Bliven <
> spe...@gm...> wrote:
> > Priyan–
> >
> > You can use the split_states command to divide it into multiple objects,
> then run the script on each state individually.
> >
> > -Spencer
> >
> > On Thu, Jan 28, 2016 at 3:45 AM, ccp4 pymol <ccp...@gm...>
> wrote:
> > Hi
> >
> > I have a multi-state object loaded in PyMOL which represents transition
> of a domain from one orientation to the other. I tried using
> "show_bumps.py" to bring up clashes during the transition but the cgo that
> is written out shows clashes only for the first state. Am I doing something
> wrong or should we pass additional commands to show clashes for all states.
> Kindly post your replies with help/suggestions in this regard.
> >
> > Thank you
> >
> > Best Regards
> > Priyan
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

would something like these work for you?

fetch 1rna, async=0
as cartoon
set cartoon_ring_mode, 1
cartoon skip
show sticks
set cartoon_ladder_mode, 0

> On Jan 28, 2016, at 6:28 PM, COSTA Maria <mar...@i2...> wrote:
> 
> Hi,
> 
> I would like to know if it is possible to have the rings filled for the nucleobases (or nucleobases + riboses) while being simply in the mode "stick" and not in the "cartoon" mode.
> 
> Many thanks for your answers,
> 
> 
> Maria,
> 
> I2BC - CNRS
> France
> ------------------------------------------------------------------------------
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Hi Spencer & Priyan,

I've updated the show_bumps script to work with multi-state objects. Please re-download.

Cheers,
  Thomas

On 28 Jan 2016, at 06:15, Spencer Bliven <spe...@gm...> wrote:

> You can automate generating the bump objects:
> 
> split_states *,prefix=split_
> for n in cmd.get_object_list("(split_*)"): show_bumps(n, "bump_"+n);
> 
> However, unfortunately the bump cgo objects don't seem to be able to be combined into a multi-state object (e.g. with `for n in cmd.get_object_list("(split_*)"): cmd.create("bumps","bump_"+n,target_state=-1)`). Thus you might have to generate your movie using some python loops to enable/disable the bumps for each frame, if you want to automate it.
> 
> -Spencer
> 
> On Thu, Jan 28, 2016 at 11:25 AM, ccp4 pymol <ccp...@gm...> wrote:
> Dear Spencer
> 
> Thank you for the suggestion. Well, I actually wanted to do it as a part of making a movie, so would have liked some automation.
> 
> Thank you.
> 
> Best Regards
> Priyan 
> 
> On Thu, Jan 28, 2016 at 2:39 PM, Spencer Bliven <spe...@gm...> wrote:
> Priyan–
> 
> You can use the split_states command to divide it into multiple objects, then run the script on each state individually.
> 
> -Spencer
> 
> On Thu, Jan 28, 2016 at 3:45 AM, ccp4 pymol <ccp...@gm...> wrote:
> Hi
> 
> I have a multi-state object loaded in PyMOL which represents transition of a domain from one orientation to the other. I tried using "show_bumps.py" to bring up clashes during the transition but the cgo that is written out shows clashes only for the first state. Am I doing something wrong or should we pass additional commands to show clashes for all states. Kindly post your replies with help/suggestions in this regard.
> 
> Thank you
> 
> Best Regards
> Priyan

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi,

I would like to know if it is possible to have the rings filled for the nucleobases (or nucleobases + riboses) while being simply in the mode "stick" and not in the "cartoon" mode.

Many thanks for your answers,


Maria,

I2BC - CNRS
France

You can automate generating the bump objects:

split_states *,prefix=split_
for n in cmd.get_object_list("(split_*)"): show_bumps(n, "bump_"+n);

However, unfortunately the bump cgo objects don't seem to be able to be
combined into a multi-state object (e.g. with `for n in
cmd.get_object_list("(split_*)"):
cmd.create("bumps","bump_"+n,target_state=-1)`). Thus you might have to
generate your movie using some python loops to enable/disable the bumps for
each frame, if you want to automate it.

-Spencer

On Thu, Jan 28, 2016 at 11:25 AM, ccp4 pymol <ccp...@gm...> wrote:

> Dear Spencer
>
> Thank you for the suggestion. Well, I actually wanted to do it as a part
> of making a movie, so would have liked some automation.
>
> Thank you.
>
> Best Regards
> Priyan
>
> On Thu, Jan 28, 2016 at 2:39 PM, Spencer Bliven <spe...@gm...>
> wrote:
>
>> Priyan–
>>
>> You can use the split_states
>> <" rel="nofollow">http://pymolwiki.org/index.php/Split_states> command to divide it into
>> multiple objects, then run the script on each state individually.
>>
>> -Spencer
>>
>> On Thu, Jan 28, 2016 at 3:45 AM, ccp4 pymol <ccp...@gm...> wrote:
>>
>>> Hi
>>>
>>> I have a multi-state object loaded in PyMOL which represents transition
>>> of a domain from one orientation to the other. I tried using
>>> "show_bumps.py" to bring up clashes during the transition but the cgo that
>>> is written out shows clashes only for the first state. Am I doing something
>>> wrong or should we pass additional commands to show clashes for all states.
>>> Kindly post your replies with help/suggestions in this regard.
>>>
>>> Thank you
>>>
>>> Best Regards
>>> Priyan
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>> Monitor end-to-end web transactions and take corrective actions now
>>> Troubleshoot faster and improve end-user experience. Signup Now!
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>>> _______________________________________________
>>> PyMOL-users mailing list (PyM...@li...)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pym...@li...
>>>
>>
>>
>

Dear Spencer

Thank you for the suggestion. Well, I actually wanted to do it as a part of
making a movie, so would have liked some automation.

Thank you.

Best Regards
Priyan

On Thu, Jan 28, 2016 at 2:39 PM, Spencer Bliven <spe...@gm...>
wrote:

> Priyan–
>
> You can use the split_states <" rel="nofollow">http://pymolwiki.org/index.php/Split_states>
> command to divide it into multiple objects, then run the script on each
> state individually.
>
> -Spencer
>
> On Thu, Jan 28, 2016 at 3:45 AM, ccp4 pymol <ccp...@gm...> wrote:
>
>> Hi
>>
>> I have a multi-state object loaded in PyMOL which represents transition
>> of a domain from one orientation to the other. I tried using
>> "show_bumps.py" to bring up clashes during the transition but the cgo that
>> is written out shows clashes only for the first state. Am I doing something
>> wrong or should we pass additional commands to show clashes for all states.
>> Kindly post your replies with help/suggestions in this regard.
>>
>> Thank you
>>
>> Best Regards
>> Priyan
>>
>>
>> ------------------------------------------------------------------------------
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> Monitor end-to-end web transactions and take corrective actions now
>> Troubleshoot faster and improve end-user experience. Signup Now!
>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
>

Priyan–

You can use the split_states <" rel="nofollow">http://pymolwiki.org/index.php/Split_states>
command to divide it into multiple objects, then run the script on each
state individually.

-Spencer

On Thu, Jan 28, 2016 at 3:45 AM, ccp4 pymol <ccp...@gm...> wrote:

> Hi
>
> I have a multi-state object loaded in PyMOL which represents transition of
> a domain from one orientation to the other. I tried using "show_bumps.py"
> to bring up clashes during the transition but the cgo that is written out
> shows clashes only for the first state. Am I doing something wrong or
> should we pass additional commands to show clashes for all states. Kindly
> post your replies with help/suggestions in this regard.
>
> Thank you
>
> Best Regards
> Priyan
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Hi

I have a multi-state object loaded in PyMOL which represents transition of
a domain from one orientation to the other. I tried using "show_bumps.py"
to bring up clashes during the transition but the cgo that is written out
shows clashes only for the first state. Am I doing something wrong or
should we pass additional commands to show clashes for all states. Kindly
post your replies with help/suggestions in this regard.

Thank you

Best Regards
Priyan

Hi Joel,


I had the same problem recently and Schrodinger released a patched version for this (v 1.8.0.2). If you go to the download page (I'm assuming as you use Windows you pay for the binary) it should be there.


best,

Iain


________________________________
From: Joel Tyndall <joe...@ot...>
Sent: Wednesday, January 27, 2016 5:51 PM
To: pym...@li...
Subject: [PyMOL] Pymol crashes with older pse files

Hi,

Having used Pymol for over a decade, I have a lot of (session) files from previous releases of Pymol. Unfortunately I am no longer able to open them in 1.8.0.0 on a windows 10 machine either from File open session or simply double clicking. (pymol.exe has stopped working). I am not convinced it works on a windows 8 machine either but it they do work on windows 7 on 1.7.2.0 release. When upgraded to 1.8.0 on windows 7 PyMOL crashes. Is there any fix for this or am I stuck with the problem?

J


Joel Tyndall | BSc(Hons) PhD

Associate Professor in Medicinal Chemistry
New Zealand's National School of Pharmacy | Te Kura Matauraka Wai-whakaora
University of Otago | Te Whare Wananga o Otago
PO Box 56 9054
Dunedin | Otepoti
New Zealand | Aotearoa
Ph: 64 3 479 7293
Skype: jtyndall
Website | pharmacy.otago.ac.nz

Hi,

Having used Pymol for over a decade, I have a lot of (session) files from previous releases of Pymol. Unfortunately I am no longer able to open them in 1.8.0.0 on a windows 10 machine either from File open session or simply double clicking. (pymol.exe has stopped working). I am not convinced it works on a windows 8 machine either but it they do work on windows 7 on 1.7.2.0 release. When upgraded to 1.8.0 on windows 7 PyMOL crashes. Is there any fix for this or am I stuck with the problem?

J


Joel Tyndall | BSc(Hons) PhD

Associate Professor in Medicinal Chemistry
New Zealand’s National School of Pharmacy | Te Kura Mātauraka Wai-whakaora
University of Otago | Te Whare Wānanga o Otāgo
PO Box 56 9054
Dunedin | Ōtepoti
New Zealand | Aotearoa
Ph: 64 3 479 7293
Skype: jtyndall
Website | pharmacy.otago.ac.nz

Dear pymol users,

I have 2 ligand molecules having similar backbone. There is little
difference between them. When I load them in pymol, I have following figure:
https://www.dropbox.com/s/k4g53p0qoxp58zs/pymol.png?dl=0

I want to have these 2 ligands in superimposed form such as following:
https://www.dropbox.com/s/v75uhrghy4johjy/pymol_2.png?dl=0

Please guide me to do that.

Best,

Dear Tsjerk,

Thanks! simply including
if '-c' in invocation._argv
in the script works fine for me,

Best,
Folmer

2016-01-27 12:43 GMT+01:00 Tsjerk Wassenaar <ts...@gm...>:

> Hey Folmer,
>
> You can check if '-c' not in invocation._argv
> Of course, you'd also need to check combinations, so it would be matching
> -.*c.* on the elements in _argv.
>
> There probably is a way to check for the GUI directly though.
>
> Hope it helps,
>
> Tsjerk
>
> On Wed, Jan 27, 2016 at 11:49 AM, Folmer Fredslund <fo...@gm...>
> wrote:
>
>> Hi there,
>>
>> I was wondering if there is a way to check if a .pml is being run in
>> command line mode (pymol -c), i.e. without the GUI.
>>
>> The reason I'm asking, is because I am making some scripts for figures,
>> and save the representations as scenes. It would be nice to both be able
>> to view them (running the .pml normally) and also make raytraced png's
>> when the .pml is being run in commandline mode.
>>
>> Best regards,
>> Folmer Fredslund
>>
>>
>> ------------------------------------------------------------------------------
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> Monitor end-to-end web transactions and take corrective actions now
>> Troubleshoot faster and improve end-user experience. Signup Now!
>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
>


-- 
Folmer Fredslund

Hey Folmer,

You can check if '-c' not in invocation._argv
Of course, you'd also need to check combinations, so it would be matching
-.*c.* on the elements in _argv.

There probably is a way to check for the GUI directly though.

Hope it helps,

Tsjerk

On Wed, Jan 27, 2016 at 11:49 AM, Folmer Fredslund <fo...@gm...>
wrote:

> Hi there,
>
> I was wondering if there is a way to check if a .pml is being run in
> command line mode (pymol -c), i.e. without the GUI.
>
> The reason I'm asking, is because I am making some scripts for figures,
> and save the representations as scenes. It would be nice to both be able
> to view them (running the .pml normally) and also make raytraced png's
> when the .pml is being run in commandline mode.
>
> Best regards,
> Folmer Fredslund
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Tsjerk A. Wassenaar, Ph.D.