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Re: model building with symmetry



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