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<mailto: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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