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: ferrer@lccp.ibs.fr ------------------------------------
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: ferrer@lccp.ibs.fr > ------------------------------------
-- - 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: azat@salilab.org - WWW/URL: http://salilab.org/~azat
participants (2)
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Azat Badretdinov -
Jean-Luc Ferrer