On Tue, 27 Apr 1999, Roberto Sanchez wrote:
> Hi,
>
> All these error messages point to a problem with the alignment. It is
> likely that the overlap between the two templates that make up the
> chimera is too small in the alignment (last error message) and/or that
> the structure of the overlapping region is very different (second chkaln
> and last error message). I could tell you more if you send your
> alignment file.
>
> The first chkaln message is telling you that two residues that flank a
> gap in the target (model) sequence are aligned with a pair of residues
> in the template (structure) that is more than 8 A apart, which probably
> means that the gap is incorrectly placed.
>
> I hope this helps.
>
> Best Wishes,
>
> Roberto
>
> --
> Roberto Sanchez | phone : (212) 327 7206
> The Rockefeller University | fax : (212) 327 7540
> 1230 York Avenue, Box 38 | e-mail:
> New York, NY 10021-6399 | http://salilab.org
>
>
> Tony Pemberton wrote:
> >
> > Dear Users,
> >
> > I am trying to produce a chimeric model as in FAQ number 4.
> > However I am getting the following error using Modeller release 4:-
> >
> > >> CHECK_ALIGNMENT:
> >
> > chkaln___> Checking pairwise structural superpositions:
> > Equivalent CA pairs with distance difference larger than 6.0
> > angstroms:
> >
> > ALN_POS TMPL1 TMPL2 RID1 RID2 NAM1 NAM2 DIST
> > ----------------------------------------------------
> >
> > chkaln___> Checking structure-sequence alignments:
> > Implied target CA(i)-CA(i+1) distances longer than 8.0
> > angstroms:
> >
> > ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
> > ----------------------------------------------
> >
> > << end of CHECK_ALIGNMENT.
> >
> > fit2xyz_E> number of equivalent positions < 3: 2
> > recover__> MODELLER_STATUS >= STOP_ON_ERROR: 1 1
> >
> > Can someone tell what this error means,
> >
> > Regards,
> >
> > Tony Pemberton
> >
Roberto,
Correct!! - Thanks for the advice,
Tony Pemberton
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Mr. A.J.Pemberton Tel: +121-414-3388
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