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.