Re: [PyMOL] Pseudoatom for a cavity

[Hitesh P. <hit...@gm...>]

Hi,

For your 2nd question:
You can make pseudoatom at Center of mass or center of geometry (for an
object or probably selection too) using the following script:
https://pymolwiki.org/index.php/Center_of_mass

In your case you mat try:

import center_of_mass

com SelectionObjectName, state=1#Create a pseudoatom representing the
Object COG and store it as "SelectionObjectName_COM"



On Thu, Jan 26, 2017 at 4:52 AM kanika sharma <ksh...@gm...> wrote:

> Dear PyMol Users,
>
> I am struggling here two things.
> 1). I want to place a pseudoatom in the charge centre of a non aromatic
> residue, like arginine.
> 2). Is it possible to place another pseudoatom in the centre of a cavity
> in the protein? I am thinking how can I define the co ordinates of the
> position where I wan t to place the pseudoatom?
>
> ​Thanks ​
>
> --
> *Best,*
>
> *Kanika*
>
>
>
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-- 
Regards,

Dr. Hitesh Patel
Post-Doctoral Fellow,
CADD Group,
Building 376, Room: 205A
Chemical Biology laboratory,
Center for Cancer Research,
National Cancer Institute,
Frederick, MD-21702

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