> 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 - Phone: (212) 327 7206 - Fax: (212) 327 7540 - E-mail: azat@salilab.org - WWW/URL: http://salilab.org/~azat