On Mon, Sep 19, 2011 at 12:41 PM, Jason Vertrees <jason.vertrees@schrodinger.com> 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 <lina.lastname@gmail.com> 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) Jason.Vertrees@schrodinger.com
(o) +1 (603) 374-7120



--
Best Regards,

lina