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
********************************************************************* Mr. A.J.Pemberton Tel: +121-414-3388 c/o Dept. Rheumatology, Fax: +121-414-3982 Medical School, E-mail: A.J.Pemberton@bham.ac.uk The University of Birmingham, Birmingham B15 2TT. U.K. *********************************************************************
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
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: sancher@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 > >
Roberto,
Correct!! - Thanks for the advice,
Tony Pemberton
********************************************************************* Mr. A.J.Pemberton Tel: +121-414-3388 c/o Dept. Rheumatology, Fax: +121-414-3982 Medical School, E-mail: A.J.Pemberton@bham.ac.uk The University of Birmingham, Birmingham B15 2TT. U.K. *********************************************************************
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Roberto Sanchez -
Tony Pemberton