Hi,
This warning comes from the part of the code which extracts the XH
bond vectors. It isn't related to the loading of the PDB itself -
this is essentially ScientificPython's PDB reader. So yes, this
function could be modified to skip proline residues. The problem here
is that there is no standardised notation for amino acids in relax and
the residue label can be anything at all! This allows for greater
flexibility in handling non-protein molecules, but makes it more
difficult for catching proline amino acids. Maybe this could be done
at the level for the ScientificPython PDB data structure. I think
this might require an abstraction of the PDB reader and relax through
a new API. That way there could be a ScientificPython specific
function, say return_vector(atom1=None, atom2=None) which returns the
required vectors. Then when a new PDB reader (or CIF, etc. reader) is
added, then they can have their own return_vector() functions. This
is all 1.3 line ideas though.
Regards,
Edward
On Feb 8, 2008 4:29 PM, Sebastien Morin <sebastien.morin.1@xxxxxxxxx> wrote:
Hi,
I noticed that, when loading a PDB file for nuclei N analysis, the
proline residues give rise to a warning concerning the fact that no
amide protons are found... For example :
===================
RelaxWarning: The atom H could not be found for residue 62
===================
This isn't a really important issue. However, the PDB loading function
could be modified slightly to avoid it looking for atoms that can't exist...
What do you think of this idea ?
Séb
--
Sebastien Morin
Etudiant au PhD en biochimie
Laboratoire de resonance magnetique nucleaire
Dr Stephane Gagne
CREFSIP (Universite Laval, Quebec, CANADA)
1-418-656-2131 #4530
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Re: Proline residues in 3D structures