RE: [PyMOL] Saving PDB with CONECT information

[Warren D. <wa...@de...>]

Hi Alan,

Hmm...you need to use "nt_arg" and "ct_glu" fragment names.  Otherwise, =
you won't get the C-terminal oxygen.

Cheers,
Warren

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> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of Alan
> Sent: Monday, March 20, 2006 12:16 PM
> To: Warren DeLano
> Cc: Pymol
> Subject: Re: [PyMOL] Saving PDB with CONECT information
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> Thanks a lot Warren.
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> If you allow me, my script to build sequences of 3 peptides=20
> is almost done. I could even use sculpt to improve my=20
> molecules structures.
>=20
> For the moment I am missing just one thing. I want to make=20
> the N-term and C-term (NH3+ and COO-) automatically for all=20
> 20 tripeptide. I know how to to do it by mouse, but how to=20
> 'add hydrogens' and 'make pk1 positive', e. g., by command?
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> Thanks a lot for PyMol.
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> Cheers,
> Alan
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> On 20/03/06, Warren DeLano <wa...@de...> wrote:
> > Alan,
> >
> > > Is PyMol able to save the built protein/molecule in a PDB=20
> file with=20
> > > CONECT information. If so, how to do it?
> >
> > Yes,
> >
> > set pdb_conect_all
> >
> > before saving the pdb file in order to get a PDB file with explicit=20
> > connectivity and valences for all atoms.
> >
> > Cheers,
> > Warren
> >
> > --
> > Warren L. DeLano, Ph.D.
> > Principal Scientist
> >
> > . DeLano Scientific LLC
> > . 400 Oyster Point Blvd., Suite 213
> > . South San Francisco, CA 94080 USA
> > . Biz:(650)-872-0942  Tech:(650)-872-0834 . Fax:(650)-872-0273 =20
> > Cell:(650)-346-1154 . mailto:wa...@de...
> >
> >
> > > -----Original Message-----
> > > From: pym...@li...
> > > [mailto:pym...@li...] On Behalf Of Alan
> > > Sent: Monday, March 20, 2006 11:39 AM
> > > To: Pymol
> > > Subject: [PyMOL] Saving PDB with CONECT information
> > >
> > > Hello List!
> > >
> > > Is PyMol able to save the built protein/molecule in a PDB=20
> file with=20
> > > CONECT information. If so, how to do it?
> > >
> > > Thanks in advance for any help.
> > >
> > > Cheers,
> > > Alan
> > > --
> > > Alan Wilter S. da Silva, D.Sc. - Research Associate Department of=20
> > > Biochemistry, University of Cambridge.
> > > 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> > >
> > >
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> --
> Alan Wilter S. da Silva, D.Sc. - Research Associate=20
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
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