Hi Michael
I think a more elegant solution is to treat the chains separately. If you want them to stay the same you can apply restraints. Thus the alignment file might look like this
>P1;candida_dimer_1st sequence:candida_dimer_1st:::: ----------------------M KIVLVL------YDAGKHAADE-EKLYGCTENKLGIANWLKDQGHELITT SDKEGGNSVLDQHIPDADIIITTPFHPAYITKERIDKAKKLKLVVVAGVG SDHIDLDYINQTGKKISVLEVTGSNVVSVAEHVVMTMLVLVRNFVPAHEQ IINHDWEVAAIAKDAYDIEGKTIATIGAGRIGYRVLERLVPFNPKELLYY DYQALPKDAEEKVGARRVENIEELVAQADIVTVNAPLHAGTKGLINKELL SKFKKGAWLVNTARGAICVAEDVAAALESGQLR GYGGDVWFPQTAPKDHPWRDMRNKYGAGNAMTPHYSGTTLDAQTRYAQG TKNILESFFTGKFDYRPQDIILLNGEYVTKAYGKHDKK------- / ----------------------M KIVLVL------YDAGKHAADE-EKLYGCTENKLGIANWLKDQGHELITT SDKEGGNSVLDQHIPDADIIITTPFHPAYITKERIDKAKKLKLVVVAGVG SDHIDLDYINQTGKKISVLEVTGSNVVSVAEHVVMTMLVLVRNFVPAHEQ IINHDWEVAAIAKDAYDIEGKTIATIGAGRIGYRVLERLVPFNPKELLYY DYQALPKDAEEKVGARRVENIEELVAQADIVTVNAPLHAGTKGLINKELL SKFKKGAWLVNTARGAICVAEDVAAALESGQLR GYGGDVWFPQTAPKDHPWRDMRNKYGAGNAMTPHYSGTTLDAQTRYAQG TKNILESFFTGKFDYRPQDIILLNGEYVTKAYGKHDKK------- * >P1;2nad_doubleA_noHET structureX:2nad_doubleA_noHET:1:A:391:B AKVLCVLYDDPVDGYPKTYARDD LPKIDHYPGGQTLPTPKAIDFTPGQLLGSVSGELGLRKYLESNGHTLVVT SDKDGPDSVFERELVDADVVISQPFWPAYLTPERIAKAKNLKLALTAGIG SDHVDLQSAID--RNVTVAEVTYCNSISVAEHVVMMILSLVRNYLPSHEW ARKGGWNIADCVSHAYDLEAMHVGTVAAGRIGLAVLRRLAPFD-VHLHYT DRHRLPESVEKELNLTWHATREDMYPVCDVVTLNCPLHPETEHMINDETL KLFKRGAYIVNTARGKLCDRDAVARALESGRLA GYAGDVWFPQPAPKDHPWRTMP-----YNGMTPHISGTTLTAQARYAAG TREILECFFEGR-PIRDEYLIVQGGALAGTGAHSYSKGNATGGSE / AKVLCVLYDDPVDGYPKTYARDD LPKIDHYPGGQTLPTPKAIDFTPGQLLGSVSGELGLRKYLESNGHTLVVT SDKDGPDSVFERELVDADVVISQPFWPAYLTPERIAKAKNLKLALTAGIG SDHVDLQSAID--RNVTVAEVTYCNSISVAEHVVMMILSLVRNYLPSHEW ARKGGWNIADCVSHAYDLEAMHVGTVAAGRIGLAVLRRLAPFD-VHLHYT DRHRLPESVEKELNLTWHATREDMYPVCDVVTLNCPLHPETEHMINDETL KLFKRGAYIVNTARGKLCDRDAVARALESGRLA GYAGDVWFPQPAPKDHPWRTMP-----YNGMTPHISGTTLTAQARYAAG TREILECFFEGR-PIRDEYLIVQGGALAGTGAHSYSKGNATGGSE
and at the end of your top file you put something like this
SUBROUTINE ROUTINE = 'special_restraints'
# Try to put symmetry restraints here # This is called from __homcsr after other restraints set up
SET RES_TYPES = 'ALL' SET ATOM_TYPES = 'ALL' SET SELECTION_STATUS = 'INITIALIZE' SET SELECTION_SEARCH = 'SEGMENT'
SET SYMMETRY_WEIGHT = 0.5 PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = '1:' '364:' PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = '365:' '728:' DEFINE_SYMMETRY ADD_SYMMETRY = on off
RETURN END_SUBROUTINE
Residues 1-364 are the first chain and 365-728 the second chain of the output homodimer.
Good luck
Daniel
+-------------------------------------------------------------------------+ | Dr Daniel John Rigden | | CENARGEN/EMBRAPA | e-mail: daniel@cenargen.embrapa.br | | Parque Estacao Biologica | http://www.cenargen.embrapa.br | | PqEB - Final - Av. W3 Norte | Phone: +55 (61)448-4741 | | 70770-900, Brasilia-D.F.-BRAZIL | Fax: +55 (61)340-3658 | +-------------------------------------------------------------------------+
On Thu, 25 Jul 2002, Michael Buck wrote:
> I have a question about modelling dimers. What I am trying to do is model > a homodimer. I have tried to few things that might work, but I am not > really sure. What I did: > 1. Edited the pdb file for the template, making it all one subunit > 2. My alignment file has the 60 amino acids from the first dimer > then chain of glycines then next 60 amino acids from the second dimer. > 3. After I model, remove the chain of glycines and add back the B > domain letter to the pdb file. > > The models look good. What does the group think? Will these models be > accurate? Will the restraints between the two dimers be included in the > models? Can I edit the restraints to remove the bad restraints located at > the end of the first dimer and beginning of the second? > > > > > > Below is the alignment: I edited the 1a0a template change B domain to A and > adjusting the amino acid numbers. > >P1;1a0aSP > structureX:1a0aSP:1:A:112:A:Pho4:yeast: 2.00:-1.00 > MKRESHKHAEQARRNRLAVALHELASLIPAEWKQQN---VSAAPSKATTVEAACRYIRHLQQNGST--------------MKRESHKHAEQARRNRLAVALHELASLIPAEWKQQN---VSAAPSKATTV* > >P1;1hlo > sequence:1hloModel: : : ::Max:Human: 2.00:-1.00 > DKRAHHNALERKRRDHIKDSFHSLRDSVP--SLQGE------KASRAQILDKATEYIQYMGGGGGGGGGGGGGGGGGGGGDKRAHHNALERKRRDHIKDSFHSLRDSVP--SLQGE------KASRAQIL* > > > > > > > > ************************************************ > Michael Buck > NCSU Genetics > mjbuck@unity.ncsu.edu > Phone (919)515-5759 > Fax (919)515-3355 > http://www4.ncsu.edu/~mjbuck > ************************************************* > >