[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: Problem with chimera model



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

*********************************************************************
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.
*********************************************************************