Re: [PyMOL] How to print sequence based on structure

[lina <lin...@gm...>]

On Mon, Sep 19, 2011 at 12:41 PM, Jason Vertrees <
jas...@sc...> wrote:

> Hi Lina,
>
> First, download the one-letter and three-letter amino acid converters
> (http://www.pymolwiki.org/index.php/Aa_codes) and run it or copy/paste
> it into PyMOL. It's nice to have these in your ~/.pymolrc. Then, try
> something like this:
>

Hi Jason,

Thanks for your answering.

Another question here,

can I show the whole residue as a ball, and different residues connect by
(virtual) bonds.

Just curious.

Thanks again for your help,


>
> # fetch a protein
>
> fetch 1rx1, async=0
>
> # hide all
>
> hide
>
> # show ball-and-stick for the main chain
>
> preset.ball_and_stick("n. C+O+N+CA")
>
> # hide the solvent
>
> hide everything, solvent
>
> # show the labels
>
> label vis, one_letter[resn]
>
> Cheers,
>
> -- Jason
>
>
> On Sat, Sep 17, 2011 at 12:48 PM, lina <lin...@gm...> wrote:
> > Hi,
> >
> > Is it possible to output the sequence roughly following the skeleton of
> protein structure?
> >
> > Or are there some other good way handling it.
> >
> > I tried aline (seem this name) before and also manually. It's headache to
> arrange large molecules.
> >
> > Thanks for any suggestions.
> >
> > Lina
> >
> ------------------------------------------------------------------------------
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>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) Jas...@sc...
> (o) +1 (603) 374-7120
>



-- 
Best Regards,

lina