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.
> 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
participants (2)
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Azat Badretdinov
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Derek Smith