Re: [PyMOL] Pymol spheres/circles

[Sampson, Jared M.]

Hi Laura -

You can also choose single atom selection mode through the menu: click Mouse > 
Selection mode > Atoms and then click your alpha carbon atom.  However, it can 
be tricky to hit the right atom if you're only looking at a cartoon 
representation, so I usually prefer to use the PyMOL command line as Osvaldo 
mentioned with something like:

```
select mutant, myprotein and resi 2
show spheres, mutant and name CA
```

Hope that helps.

Cheers,
Jared



On Aug 30, 2016, at 8:18 AM, Smith, Laura 
> wrote:

Hi,

I’m pretty new to Pymol and not that great with all the syntax etc.

I am wanting to easily show where a mutation is located in  cartoon model. I’ve 
tried to label the residues with spheres but it generates more than one dot and 
that’s not what I want. I just want one single sphere/circle/dot localised to 
an atom on the structure for me to label myself.

Basically like figure 2A in this paper >> 
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1326319/

Thanks,
Laura


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Re: [PyMOL] Pymol spheres/circles

[Osvaldo Martin]

Hi Laura,

Read here

how to select a single atom using the GUI. Or using the command line and
the selection albegra 
do something like:

select mutant, resi 2 and name ca

This will create a selection named mutant consisting on the alpha carbon of
residue 2.

Once the atom is selected you can choose the most convenient representation
for you, like an sphere.

Cheers,
Osvaldo.

On Tue, Aug 30, 2016 at 2:18 PM, Smith, Laura 
wrote:

Hi,
>
>
>
> I’m pretty new to Pymol and not that great with all the syntax etc.
>
>
>
> I am wanting to easily show where a mutation is located in  cartoon model.
> I’ve tried to label the residues with spheres but it generates more than
> one dot and that’s not what I want. I just want one single
> sphere/circle/dot localised to an atom on the structure for me to label
> myself.
>
>
>
> Basically like figure 2A in this paper >> http://www.ncbi.nlm.nih.gov/
> pmc/articles/PMC1326319/
>
>
>
> Thanks,
>
> Laura
>
>
>
>
>
> 
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>
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[PyMOL] Pymol spheres/circles

[Smith, Laura]

Hi,

I'm pretty new to Pymol and not that great with all the syntax etc.

I am wanting to easily show where a mutation is located in  cartoon model. I've 
tried to label the residues with spheres but it generates more than one dot and 
that's not what I want. I just want one single sphere/circle/dot localised to 
an atom on the structure for me to label myself.

Basically like figure 2A in this paper >> 
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1326319/

Thanks,
Laura


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