Re: [PyMOL] representation of residue sidechain within a beta strand?

[Yufeng T. <yuf...@gm...>]

Hi Tomas,

I noticed this setting is not working when
preset.pretty(selection='all') has been invoked, that is, whether
cartoon_side_chain_helper is set to on or off, the side chain is
disconnected. Do you know what is changed when preset.pretty() is
called?

The reason I want to call preset.pretty() is that if this is not
called, the sticks representation of an isopeptide cannot be properly
displayed (no sticks shown for the isopeptide bond), a bit of a
dilemma.

Thanks,

Yufeng


On Mon, Jan 18, 2021 at 3:35 AM Tomas Malinauskas
<tom...@gm...> wrote:
>
> Hi Emilia,
>
> You might try the following:
> set cartoon_side_chain_helper, on
>
> Hope that helps,
> Tomas
>
> On Mon, Jan 18, 2021 at 7:52 AM Emilia C. Arturo (Emily)
> <ecg...@gm...> wrote:
> >
> > Hi All,
> >
> > I'm wondering if anyone here knows how to represent an amino acid residue side chain that resides within a beta strand in stick representation such that the residue is linked in space with the backbone. This works fine when representing as sticks a residue that is within a loop or helix, but not within a strand; there it just sticks out into space, which looks awful if the figure is not turned 'just so' so that the viewer cannot see the space. I am using version 2.4.0 on my Mac.
> >
> > Regards,
> > Emilia.
> >
> > --
> > "Study as if you were going to live forever; live as if you were going to die tomorrow." - Maria Mitchell
> >
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