David,
You found a bug -- it turns out PyMOL was getting confused by
the presence of a "P" atom in P-tyr. It thought the residue contained
both protein and DNA, and so the cartoon had an extra gap.
The following workaround should get you a complete cartoon with 1fmk.
Future versions of PyMOL should not suffer from this problem.
alter all.type='ATOM'
alter name P,name='P1'
sort
Thanks for your help in quashing that bug!
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
> -----Original Message-----
> From: David A. Horita [mailto:dhor...@wfubmc.edu]
> Sent: Wednesday, August 06, 2003 5:27 AM
> To: Warren L. DeLano
> Subject: RE: [PyMOL] cartoons through nonstandard residues
>
> Warren,
> Thanks for the reply, but I still don't get the cartoon running
through
> the phosphotyrosine. I've tried it on Src (1fmk.pdb), and still get a
> break between residues Gln526, Ptr 527 and Gln 528.
> Regards,
> David Horita
>
> > -----Original Message-----
> > From: Warren L. DeLano [mailto:war...@delanoscientific.com]
> > Sent: Tuesday, August 05, 2003 7:17 PM
> > To: David A. Horita; pymol-users@lists.sourceforge.net
> > Subject: RE: [PyMOL] cartoons through nonstandard residues
> >
> >
> > David,
> >
> > The problem: PyMOL sorts PDB hetatms apart from molecules. The
> > solution:
> >
> > alter all, type='ATOM'
> > sort
> > rebuild
> >
> > I'm thinking about disabling this behavior before the next
release...
> >
> > Cheers,
> > Warren
> >
> > --
> > mailto:war...@delanoscientific.com
> > Warren L. DeLano, Ph.D.
> > Principal Scientist
> > DeLano Scientific LLC
> > Voice (650)-346-1154
> > Fax (650)-593-4020
> > -----Original Message-----
> > From: pymol-users-ad...@lists.sourceforge.net
> > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
> > David A. Horita
> > Sent: Tuesday, August 05, 2003 1:53 PM
> > To: pymol-users@lists.sourceforge.net
> > Subject: [PyMOL] cartoons through nonstandard residues
> >
> > Hi,
> > When I try to draw a cartoon through the backbone of a
> > nonstandard residue (in this case, phosphotyrosine), the
> > cartoon strand stops prior to the PTR and starts after. How
> > do I get a continuous strand through the phosphotyrosine
> > backbone (or other residues, in the general case)?
> > Ribbons seem to go through the PTR without problem, and
> > selenomets don't seem to cause trouble, either. Thanks, David Horita
> > -----------------------------
> > David A. Horita, Ph.D.
> > Department of Biochemistry
> > Wake Forest University School of Medicine
> > Winston-Salem, NC 27157-1016
> > Tel: 336 713-4194
> > Fax: 336 716-7671
> > email: dhor...@wfubmc.edu
> > web: http://www.wfubmc.edu/biochem/faculty/Horita/
> >
> >
> >
