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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