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simmol uses the amide proton to define the peptide plane coordinate system, so in order to use the built-in coordinate system you need to use the "maddprotons $m -amide" command... For Proline, it also adds an amide proton, but only internally, so it shouldn't be visible or selectable if I remember right.
Otherwise, the only way to do this is to define your own coordinate system using "msetcoordsys" and then add the carbonyl tensor... See the original SIMMOL paper for a similar example, where we added 15N tensors in the histidine sidechain.
Thomas
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Thomas Vosegaard, Assoc. Prof.
Center for Insoluble Protein Structures (inSPIN)
Department of Chemistry and
Interdisciplinary Nanoscience Center (iNANO)
Langelandsgade 140, DK-8000 Aarhus C, Denmark
Tel: +45 8942 3866, Cell: +45 6020 2639, Fax: +45 8619 6199
E-mail: tv@..., Web: http://www.chem.au.dk/~tv
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On Jun 16, 2008, at 14:22 , Loren Andreas wrote:
Hi simmol users,
I have encountered an problem when defining a csa on proline C'. if
I add amide protons there is no problem, however, if I directly use a
pdb structure (with protons) I get an error for the proline residue.
Is there a way to define the csa without adding a dummy proton atom
to the proline? It is not very satisfying to see an amide proton on
proline.
any help would be much appreciated.
-Andreas
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