Re: Problem with chimera model

[Roberto Sanchez <sancher AT rockefeller.edu>]

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: sancher AT rockvax.rockefeller.edu
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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