Re: [PyMOL] Pseudoatom for a cavity

[Sampson, J. M. <jm...@cu...>]

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 <ksh...@gm...<mailto:ksh...@gm...>> 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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