Re: [PyMOL] Stacking Interactions

[Osvaldo Martin]

Hi Amali,

I am not aware that PyMOL has this feature implemented out-of-the-box.
Nevertheless this can be done with PyMOL. A crude approximation will be to
measure the distance between the center of aromatic rings and consider a
pi-pi stacking for distances shorter than a threshold value. A better model
will probably include a distance threshold and one or two angles in the
definition.

Are you trying to estimate pi-pi stacking interactions in general or for a
particular system?

Cheers,
Osvaldo.

On Tue, Nov 10, 2015 at 5:43 AM, Amali Guruge  wrote:

> Dear all,
>
> I want to know can we identify p-p stacking interactions using PyMOL?
>
> Can anyone help me?
>
> Thank you in advance.
>
>
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Re: [PyMOL] Stacking Interactions

[Albert]

I think the major concern is how Pymol depicts the pi-pi stacking Of 
course we can identify such interaction immediately as soon as we open 
the system in Pymol.


However there is no any  components to indicate this, eg: we can depict 
the H-bond with a dash between two atoms but how could pi-pi interaction 
be depicted?




On 11/10/2015 07:03 AM, Osvaldo Martin wrote:

Hi Amali,

I am not aware that PyMOL has this feature implemented out-of-the-box. 
Nevertheless this can be done with PyMOL. A crude approximation will 
be to measure the distance between the center of aromatic rings and 
consider a pi-pi stacking for distances shorter than a threshold 
value. A better model will probably include a distance threshold and 
one or two angles in the definition.


Are you trying to estimate pi-pi stacking interactions in general or 
for a particular system?


Cheers,
Osvaldo.


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[PyMOL] Stacking Interactions

[Amali Guruge]

Dear all,

I want to know can we identify p-p stacking interactions using PyMOL?

Can anyone help me?

Thank you in advance.
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[PyMOL] Using Python 3.4.3 Shell

[Tom Aharoni]

Hey :)

I would like to work with pymol commands such as
cmd.distance() etc using Python 3.4.3 Shell.

However when I try "import pymol" i get this message:

Traceback (most recent call last):
  File "", line 1, in 
import pymol
ImportError: No module named 'pymol'

I would very appreciate your help.


-- 
*Tom Aharoni*
*PhD student @ Tel Aviv Uni.*


*kuwari.tau.ac.il/Home.html *
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Re: [PyMOL] Using Python 3.4.3 Shell

[Justin Lecher]

On 09/11/15 09:05, Tom Aharoni wrote:
> Hey :)
> 
> I would like to work with pymol commands such as 
> cmd.distance() etc using Python 3.4.3 Shell. 
> 
> However when I try "import pymol" i get this message:
> 
> Traceback (most recent call last):
>   File "", line 1, in 
> import pymol
> ImportError: No module named 'pymol'
> 
> I would very appreciate your help.
> 

Hi,

simply you can't right now as pymol is not python3 ready yet.

Justin


-- 
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Institute of Complex Systems
ICS-6 Structural Biochemistry
Research Centre Juelich
52425 Juelich, Germany
phone: +49 2461 61 2117




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developed by Facebook, enables you to easily query your data on Hadoop in a 
more interactive manner. Teradata is also now providing full enterprise
support for Presto. Download a free open source copy now.
http://pubads.g.doubleclick.net/gampad/clk?id=250295911=/4140___
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