Dear Jean-Luc!
The problem is that two templates your specified in the alignment do not
overlap in this alignment, so they cannot be structurally superposed to
produce a frame for your protein. There is no other way to do that
except manually. Trivially, it will be better to have a known structure
of some dimer...
Yours,
Azat.
Jean-Luc Ferrer wrote:
>
> Hye,
>
> I would like to build a model for a dimere (the
> 2 molecules are 2-fold axis symmetry related).
> I tried to duplicate the sequence of the monomere,
> separated by a /:
>
> >P1;acs
> sequence:acs:. :.:. :.:?: : 3.66: 0.00
> MESLKEMRKAQMSEGPAAILAIGTATPDNVFMQADYPDYYFRMTKSEHMTELKDKFRTLCEKSMIRKRHMCFSED
> FLKANPEVCKHMGKSLNARQDIAVVETPRLGNEAALKAIKEWGQPKSSITHLIFCSSAGVDMPGADYQLTRILGL
> NPSVKRMMIYQQGCYAGGTVVRLAKDLAENNKGSRVLVVCSELTAPTFRGPSPDAVDSLVGQALFADGAAALVVG
> ADPDSSIERALYYLVSASQMLLPDSDGAIEGHIREEGLTVHLKKDVPALFSANIDTPLVEAFKPLGISDWNSIFW
> IAHPGGPAILDQIEEKLGLKEDKLRASKHVMSEYGNMSSSCVLFVLDEMRSRSLQDGKSTTGQGLDWGVLFGFGP
> GLTVETIVLRSVPIEA/
> MESLKEMRKAQMSEGPAAILAIGTATPDNVFMQADYPDYYFRMTKSEHMTELKDKFRTLCEKSMIRKRHMCFSED
> FLKANPEVCKHMGKSLNARQDIAVVETPRLGNEAALKAIKEWGQPKSSITHLIFCSSAGVDMPGADYQLTRILGL
> NPSVKRMMIYQQGCYAGGTVVRLAKDLAENNKGSRVLVVCSELTAPTFRGPSPDAVDSLVGQALFADGAAALVVG
> ADPDSSIERALYYLVSASQMLLPDSDGAIEGHIREEGLTVHLKKDVPALFSANIDTPLVEAFKPLGISDWNSIFW
> IAHPGGPAILDQIEEKLGLKEDKLRASKHVMSEYGNMSSSCVLFVLDEMRSRSLQDGKSTTGQGLDWGVLFGFGP
> GLTVETIVLRSVPIEA*
>
> and create a known structure for each monomere of the template:
>
> >P1;chs1
> structureX:chs1: 1 : : 389 : :chalcone synthase: : 1.80: 0.00
> MVSVSEIRKAQRAEGPATILAIGTANPANCVEQSTYPDFYFKITNSEHKTELKEKFQRMCDKSMIKRRYMYLTEE
> ILKENPNVCEYMAPSLDARQDMVVVEVPRLGKEAAVKAIKEWGQPKSKITHLIVCTTSGVDMPGADYQLTKLLGL
> RPYVKRYMMYQQGCFAGGTVLRLAKDLAENNKGARVLVVCSEVTAVTFRGPSDTHLDSLVGQALFGDGAAALIVG
> SDPVPEIEKPIFEMVWTAQTIAPDSEGAIDGHLREAGLTFHLLKDVPGIVSKNITKALVEAFEPLGISDYNSIFW
> IAHPGGPAILDQVEQKLALKPEKMNATREVLSEYGNMSSACVLFILDEMRKKSTQNGLKTTGEGLEWGVLFGFGP
> GLTIETVVLRSVAI--/
> ---------------------------------------------------------------------------
> ---------------------------------------------------------------------------
> ---------------------------------------------------------------------------
> ---------------------------------------------------------------------------
> ---------------------------------------------------------------------------
> ----------------*
> >P1;chs2
> structureX:chs2: 1 : : 389 : :chalcone synthase: : 1.80: 0.00
> ---------------------------------------------------------------------------
> ---------------------------------------------------------------------------
> ---------------------------------------------------------------------------
> ---------------------------------------------------------------------------
> ---------------------------------------------------------------------------
> ----------------/
> MVSVSEIRKAQRAEGPATILAIGTANPANCVEQSTYPDFYFKITNSEHKTELKEKFQRMCDKSMIKRRYMYLTEE
> ILKENPNVCEYMAPSLDARQDMVVVEVPRLGKEAAVKAIKEWGQPKSKITHLIVCTTSGVDMPGADYQLTKLLGL
> RPYVKRYMMYQQGCFAGGTVLRLAKDLAENNKGARVLVVCSEVTAVTFRGPSDTHLDSLVGQALFGDGAAALIVG
> SDPVPEIEKPIFEMVWTAQTIAPDSEGAIDGHLREAGLTFHLLKDVPGIVSKNITKALVEAFEPLGISDYNSIFW
> IAHPGGPAILDQVEQKLALKPEKMNATREVLSEYGNMSSACVLFILDEMRKKSTQNGLKTTGEGLEWGVLFGFGP
> GLTIETVVLRSVAI--*
>
> and run the model.top script:
>
> > INCLUDE # Include the predefined TOP routines
> > SET ALNFILE = 'acs.align' # alignment filename
> > SET KNOWNS = 'chs1' 'chs2' # codes of the templates
> > SET SEQUENCE = 'acs' # code of the target
> > SET ATOM_FILES_DIRECTORY = '../../pdb/' # directories for input atom files
> > SET STARTING_MODEL= 1 # index of the first model
> > SET ENDING_MODEL = 1 # index of the last model
> > CALL ROUTINE = 'model' # do homology modelling
>
> and then I get the error:
>
> > 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
> > ----------------------------------------------------
> > drmsq1__W> n<2
> > drmsq3__W> n<2
> >
> > 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: 0
> recover__> MODELLER_STATUS >= STOP_ON_ERROR: 1 1
>
> I guess it certainly not the right way to do that.
> So, if somebody has any suggestion...
>
> Thanks
>
> Jean-Luc
>
> ------------------------------------
> Jean-Luc FERRER
> Structural Biology Laboratory
> The Salk Institute for Biol. Studies
> P.O. Box 85800
> San Diego, California 92186-5800
> USA
>
> phone: (619) 453-4100 ext 1535/1383
> fax: (619) 452-3683
> email:
> ------------------------------------
--
- Dr. Azat Badretdinov
- The Rockefeller Univ, Box 270
- 1230 York Ave, New York NY 10021, USA
- Phone: (212) 327 7206
- Fax: (212) 327 7540
- E-mail:
- WWW/URL: http://salilab.org/~azat