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:
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