Re: [PyMOL] Active site in Pymol

2016-09-29 Thread Julian Heinrich 
Hi,

you can use the Measurement Wizard to get distances between atoms. PyMOL
will also print the residue type in the console if you click on any atom.

Best,
Julian


On Tue, Aug 23, 2016 at 8:45 AM Farzaneh Namazifar <
f.namazifar706...@gmail.com> wrote:

> Hi Dear all;
> I am a PyMol user.  I read the PyMOL tutorial
> 
>  about
> the hydrogen bond. I need some informations about hydrogen bond like:
> 1- length of hydrogen bond between two residue
> 2- which kind of residues are in the hydrogen bond
> 3- Number of hydrogen bond in active site
> As above, I need informations about  Hydrophobicity of residues in the
> active site. and else information about pi-pi interaction in DNA... I need
> your help ...
> Best Regards.
> Thank you in advance.
>
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Re: [PyMOL] error message for forster resonance calcualtor

2016-09-29 Thread Julian Heinrich 
Hi Andina,

did you try to run 'import Forster_distance_calculator.py' from the Pymol
command line?
Have you tried to do 'run Forster_distance_calculator.py' instead, then
'forster ...' ?

Cheers,
Julian


On Mon, Sep 19, 2016 at 9:52 AM Andina Diana 
wrote:

> Hello everyone,
>
>
>
> I  have downloaded the newest version of pymol and wanted to run the
> script to calculate the Förster Resonance Energy distance R0 from the its
> wiki page (https://pymolwiki.org/index.php/Forster_distance_calculator) .
> When I import the file, it gives me following error message:
>
>
>
> Traceback (most recent call last):
>
>   File "C:\Program Files\PyMOL\\PyMOL/modules\pymol\parser.py", line 262,
> in parse
>
> exec(layer.com2+"\n",self.pymol_names,self.pymol_names)
>
>   File "", line 1, in 
>
>
>
> What should I do to not get this error message?
>
>
>
> Thank you for your help!
>
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Re: [PyMOL] Pymol Command window not displaying

2016-09-29 Thread Julian Heinrich 
Hi,

are you trying to run PyMOL remotely, i.e. via ssh from your cluster?
This might work if you forward X11 to your local machine, though I'm not
sure if it supports OpenGL.

Looking at the error message, another possibility might be a missing tcl/tk
library?

Good luck,
Julian

On Tue, Sep 20, 2016 at 7:24 AM Srikanth Gumma 
wrote:

> Hi,
>
> Can anyone help me on this regard.
>
> Thanks
>
> -Srikanth.
>
> On Thu, Sep 1, 2016 at 10:19 PM, Thomas Holder <
> thomas.hol...@schrodinger.com> wrote:
>
>> Hi Srikanth,
>>
>> Is your custom Python installation properly set up with the custom Tcl/Tk
>> installation? Does the following work and open a Tk window?
>>
>> shell> /app/python/intel/2.7.12/bin/python # path guessed
>> python> import Tkinter
>> python> Tkinter.Tk()
>>
>> If not, then I think you need to set TCL_LIBRARY and/or TK_LIBRARY
>> environment variables first.
>>
>> Hope that helps.
>>
>> Cheers,
>>   Thomas
>>
>> On 31 Aug 2016, at 00:46, Srikanth Gumma  wrote:
>>
>> > Hi,
>> >
>> > I recently installed pymol from source using python-2.7.12 in my
>> cluster. I have to install python, tcl in a non standard location as this
>> is a cluster.
>> >
>> > After successful installation of pymol, I'm facing an issue while
>> opening pymol. I'm not able to see pymol command window, and receiving the
>> below error on the console.
>> >
>> > PyMOL(TM) Molecular Graphics System, Version 1.8.2.0.
>> >  Copyright (c) Schrodinger, LLC.
>> >  All Rights Reserved.
>> >
>> > Created by Warren L. DeLano, Ph.D.
>> >
>> > PyMOL is user-supported open-source software.  Although some
>> versions
>> > are freely available, PyMOL is not in the public domain.
>> >
>> > If PyMOL is helpful in your work or study, then please volunteer
>> > support for our ongoing efforts to create open and affordable
>> scientific
>> > software by purchasing a PyMOL Maintenance and/or Support
>> subscription.
>> >
>> > More information can be found at "http://www.pymol.org;.
>> >
>> > Enter "help" for a list of commands.
>> > Enter "help " for information on a specific command.
>> >
>> >  Hit ESC anytime to toggle between text and graphics.
>> >
>> >  Detected OpenGL version prior to 2.0. Shaders and volumes unavailable.
>> >  OpenGL graphics engine:
>> >   GL_VENDOR:   Intel
>> >   GL_RENDERER: Intel(R) HD Graphics 4600
>> >   GL_VERSION:  1.4 (4.0.0 - Build 9.18.10.3272)
>> > Traceback (most recent call last):
>> >   File "/app/python/intel/pymol/lib/python/pmg_tk/__init__.py", line
>> 35, in run
>> > PMGApp(pymol_instance,skin).run(poll)
>> >   File "/app/python/intel/pymol/lib/python/pmg_tk/PMGApp.py", line 323,
>> in __init__
>> > self.root = Tk() # creates the root window for the application
>> >   File "/app/python/intel/2.7.12/lib/python2.7/lib-tk/Tkinter.py", line
>> 1815, in __init__
>> > self.tk = _tkinter.create(screenName, baseName, className,
>> interactive, wantobjects, useTk, sync, use)
>> > TclError: invalid command name "tcl_findLibrary"
>> >  Detected 24 CPU cores.  Enabled multithreaded rendering.
>> >
>> >
>> > Appreciate any help to resolve the issue.
>> >
>> > -srikanth
>>
>> --
>> Thomas Holder
>> PyMOL Principal Developer
>> Schrödinger, Inc.
>>
>>
>
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