Miguel is right.
REFMAC like all CCP4 programs expects that consecutive residues are
numbered consecutively..
If this is no t the case you need to edit the input PDB before running
REFMAc (or COOT, or xxx.... )
You can use CHAINSAW to do this probably if you have a sequence
alignment or do it by hand with COOT or PDBSET. I recommend writing the
numbering on a piece of paper. It can be easy to go wrong when there are
many gaps!
Eleanor
Miguel Ortiz-Lombardia wrote:
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Hi Bernhard,
Seems to me that is exactly the behavior you would expect with a "gap"
link.
No, perhaps misunderstanding. This is a contiguous chain,
just numbered discontinuously according to some
biological reason. So the distances are very close
to correct peptide links, and refmac in fact calls the
link a 'GAP LINK' (<-term LINK!) so it seems to have properly
identified them as close enough together?
No, "gap link" is a misnomer: it means in fact that refmac it's treating
the amino acids boundaries involved effectively as a gap, that is, as if
you would be expecting amino acids to lay in between.
Refmac5 must be assuming that you number your protein according to your
protein sequence, which is continuous. In my opinion, this is
reasonable. Instead, it should the longer sequences with respect to
which you would like to have yours numbered that should have insertion
codes (supported by refmac5). Unless you have deleted those particular
amino acid residues from your native sequence for some reason...
In any case, to solve your problem, I don't know if there is something
like a "nogap link" notation in refmac5...
Cheers,
Miguel
- --
Miguel Ortiz Lombardía
Centro de Investigaciones Oncológicas
C/ Melchor Fernández Almagro, 3
28029 Madrid, Spain
Tel. +34 912 246 900
Fax. +34 912 246 976
e-mail: [EMAIL PROTECTED]
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Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que
ce qui est fort fût juste.
Blaise Pascal, Pensées
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