Thanks Jared.
First part, is perfect. So pseudo atom lies between nitrogen atoms.
Second part, I don't have specific xyz coordinates because it is centre of
a tunnel in the protein and that's the struggle.
On Thu, Jan 26, 2017 at 10:01 PM, Sampson, Jared M. <
jms2...@cumc.columbia.edu> wrote:
> Hi Kanika -
>
> You can get more information on the wiki: https://pymolwiki.org/
> index.php/Pseudoatom.
>
> To answer your specific questions, to make a pseudoatom between the two
> terminal Ns of Arg 100 on chain A of myobj:
>
> ```
> pseudoatom my_ps1, myobj and chain A and resi 100 and name NH1+NH2
> ```
>
> and to place a pseudoatom at a specific XYZ coordinate, pass the `pos`
> parameter with a 3-tuple of floats:
>
> ```
> pseudoatom my_ps2, pos=[1.0, 2.0, 3.0]
> ```
>
> Hope that helps.
>
> Cheers,
> Jared
>
>
> On Jan 26, 2017, at 8:58 AM, kanika sharma <ksharma...@gmail.com> wrote:
>
>
>
> Dear PyMol Users,
>
> I asked this question but no body replied so I am trying again.
>
> I am struggling here two things.
> 1). I want to place a pseudo
>
> atom in the charge centre of a non aromatic residue, like arginine.
> 2). Is it possible to place
> a
> pseudo
>
> atom 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 pseudo
>
> atom?
>
> Thanks
>
> --
> *Best,*
>
> *Kanika*
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--
*Best,*
*Kanika Sharma*
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