Dear Modellers
I am trying to model some proteins with a calcium binding site. Looking
in the manual, I altered my sequence alignment as so:
FIRST-TEMPLATE--/3*
SECOND-TEMPLATE-/3*
THIRD-TEMPLATE
SEQUENCE--------/3*
When I try to model the sequence, I end up with the calcium in the
position of the next (and non-existent) c-terminal residue. Can anyone
help with this? Have I used incorrect notation for the sequences?
Also, another project I'm attempting involves adding two disulphide
restraits to a model. If I model the protein without the restraints,
PATCH_DISULFIDES finds three disulfides, and I end up with a refined
model with an objective function of ~800. When adding the special
patches, I get an unrefined model with an objective function of ~109000.
The structural alignment suggests that at least one of the cysteine
pairs are in the right positions for disulphide formation, yet just
adding that restraint gives the same result (huge objective function).
Do you have any suggestions?
Yours,
Derek.
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Derek Smith
email:
Department of Chemistry
University of York, Heslington, York. YO1 5DD United Kingdom.
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