Hi,
The wiki has a page on this:
http://www.pymolwiki.org/index.php/Peptide_Sequence
except it doesn't mention the zwitterion details. There's a link to
Robert Campbell's scripts to do this sort of thing, so maybe the
answer is there.
As for for loops, this is best in a full python script (run with
"run"). In fact, your pseudocode is almost valid python. More like:
residues =3D ("A", "C", "D", "E", "F", "G", "H" etc)
for residue in residues:
for i in range(3):
cmd._alt(residue.lower())
cmd.set_geometry ??
cmd.save(aa.pdb, "all")
Unfortunately, I'm not sure the set_geometry command is right.
gilleain torrance
On 3/14/06, Alan <ala...@gm...> wrote:
> Hello List,
>
> I would like to have any help.
>
> I want to build several 3-peptides, like AAA, FFF, KKK etc. I also
> would like to make them zwitterionics, add chain and save as a PDB
> file.
>
> I know how to do that using the graphic interface, but I what I am
> looking for is a way to do it via pymol script.
>
> Is is possible? May anyone give a idea of how create the 3-peptides
> and put right N- and C- terminals?
>
> BTW, a loop with "for" is possible in pymol scripting?
>
> Summarising, I am trying a script like this:
>
> -----------------------
> residue =3D ( ALA, ARG, etc)
>
> for res in residue:
> 'create peptide res-res-res'
> 'set NH3 in res 1 and COO- in res 3'
>
> save aa.pdb, all
> -----------------------
>
> Thanks a lot for any help.
>
> Cheers,
> Alan
> --
> Alan Wilter S. da Silva, D.Sc. - Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
>
>
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