> 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?
Let us try first stupid explanation: alignment is not correct, but you
probably already checked that 3 stands on the same position on all 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?
First I have a question: what was wrong with the "800" model?
Why do you need to add special patches? Looks like PATCH_DISULFIDES
perfectly does the job?
Azat
--
- Dr. Azat Badretdinov
- The Rockefeller Univ, Box 270
- 1230 York Ave, New York NY 10021, USA
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