pymol-users

[PyMOL] How could I modify the secondary structures after superimpose of 2 or more structure?

[yucmbuu <yu...@ga...>]

Dear All:

I made two protein models from one known pdb by using SWISS-MODEL server. I
superimpose these three pdb with pymol. However, I need to modified the
secondary structure of these structures after "procheck". How could I using
"alter" command to modified one structure at once? Is it meaningful that
RMS scores were obtained by using "align" command in pymol? Thanks for your
help.

Chung-Ming Yu
Inst. Biol. Chem.
Academia Sinica

Re: [PyMOL] How could I modify the secondary structures after superimpose of 2 or more structure?

[Tsjerk W. <ts...@gm...>]

Hi Chung-Ming Yu,

You can change the secondary structure identifiers as follows:

alter helix_selection,ss=3D'H'
alter sheet_selection,ss=3D'S'
alter loop_selection, ss=3D'L'

The RMS deviation gives you information about the quality of the fit. The
lower the number, the better the fit.

Cheers,

Tsjerk

On 10/8/05, yucmbuu <yu...@ga...> wrote:
>
> Dear All:
>
> I made two protein models from one known pdb by using SWISS-MODEL server.
> I
> superimpose these three pdb with pymol. However, I need to modified the
> secondary structure of these structures after "procheck". How could I
> using
> "alter" command to modified one structure at once? Is it meaningful that
> RMS scores were obtained by using "align" command in pymol? Thanks for
> your
> help.
>
> Chung-Ming Yu
> Inst. Biol. Chem.
> Academia Sinica
>
>
>
>
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--

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336