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
>
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> Mr. A.J.Pemberton Tel: +121-414-3388
> c/o Dept. Rheumatology, Fax: +121-414-3982
> Medical School, E-mail:
> The University of Birmingham,
> Birmingham B15 2TT.
> U.K.
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