Hi there I would like to model a multidomain protein but when I follow the instructions given in the manual I only only get a model based on the first structure in my alignment file. It totally ignores the second structure. There is no overlap between the domains. The top file and alignment file is attached. Can anyone help? Thanks!! -- Tjaart de Beer Bioinformatics and Computational Biology Unit Department Biochemistry FABI 2/BCBU building Faculty of Natural Sciences University of Pretoria Lynwood rd Pretoria South Africa 0001 Tel: +27 12 420 5802 Cell: +27 83 504 7914 Fax: +27 12 420 5800 Email: tjaart@tuks.co.za tjaartdb@absamail.co.za >P1;pf sequence:pf:1:A:611::::: METIQELILSEENKTNIAVLNLGTNDRRNAVLILETALHLVEKYLGKIINTSYLYETVPEYIVLDKK FYNLTVVVKTFVNDPLSMLVVIKYIE-ELMKRENVKEKEKFENRIIDIDILFFNDFTIFMKNIKLEKNMIYKILSKYIHLERDIKNGNDNMSKVNMDKDINLNNNNNIKKKNNNDIDCDCVDQKMNNHVNNKNYINSFRDPQEIINNMVD NIEFLSIPHVYTTHRYSILLCLNDMIPEYKHNVLNNTIRCLYNKYVSRMKEQYNINIKENNKRIYVLKDRISYLKEKTNIVGILNV-----------NYDSFSDGGIFVEPKRAVQRMFEMINEGASVIDIGGESSAPFVIPNPKISERDLVVPVL QLFQKEWNDIKNKIVKCDAKPIISIDTINYNVFKECVDNDLVDILNDISACTNNPEIIKLLKKKNKFYSVVLMHKRGNPHTMDKLTN-YDNLVYDIKNYLEQRLNFLVLNGIPRYRILFDIGLGFAKKHDQSIKLLQNIHVYDEY-----PLFIGY SRKRFIAHCMNDQNVVINTQQKLHDEQQNENKNIVDKSH-NWMFQMNYMRKDKDQLLYQKNICGGLAIASYSYYKKVDLIRVHDVLETKSVLDVLTKIDQV-* >P1;1DY3 structureX:1DY3:1:A: 158:A:::: ---------------TVAYIAIGSNLASPLEQVNAALKALGDIPESHILTVSSFYRTPPLGPQDQPD YLNAAVALET-SLAPEELLNHTQRIE-LQQGRVRK--AERWGPRTLDLDIMLFGNEVINTER-----LTVPHYDMKNRGFMLWPLFEIAPELVFPDGEMLRQILHTRAFDKLNKW----------------------------------- ------------------------------------------------------------------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------------* >P1;1eye structureX:1eye:5:A:274:A:::: ------------------------------------------------------------------- ------------------------------------------------------------------------------------------------------------------------------------------------------ ----------------------------------------------------------------------------PVQVMGVLNVTDDSFSDGGCY-----------LDLDDAVKHGLAMAAAGAGIVDVGG--------------ETSRVIPVV KELAAQG-------------ITVSIDTMRADVARAALQN-GAQMVNDVSGGRADPAMGPLLAEA--DVPWVLMHWRAVSADTPHVPVRYGNVVAEVRADLLASVADAVAAGVDPARLVLDPGLGFAKT-AQHN--WAILHALPELVATGIPVLVGA SRKRFLGALLAGPD-GVMRPTDGRD-TATAVISALAALHGAWGV------------------------------------RVHDVRASVDAIKVVEAWMGAE* INCLUDE # Include the predefined TOP routines SET PDB_EXT = '.pdb' SET ALNFILE = 'HPPK-DHPS1.ali' # alignment filename SET KNOWNS = '1eye' # codes of the templates SET KNOWNS = '1DY3' SET SEQUENCE = 'pf' # code of the target #SET HETATM_IO ='on' #SET WATER_IO = 'on' #SET TOPOLOGY_LIBRARY = $(LIB)/top_heavy.lib #SET PARAMETERS_LIBRARY = $(LIB)/par.lib SET ATOM_FILES_DIRECTORY ='/hosts/milliways/people/tjaart/home/My_Documents/Bifunctional_modelling/' # directories for input atom files SET STARTING_MODEL = 1 SET ENDING_MODEL = 5 SET OUTPUT_CONTROL = 1 1 1 1 1 #SET FINAL_MALIGN3D = 1 CALL ROUTINE = 'model' # do homology modelling SUBROUTINE ROUTINE = 'special_restraints' SET ADD_RESTRAINTS = 'on' MAKE_RESTRAINTS RESTRAINT_TYPE = 'alpha', RESIDUE_IDS = '594' '607' END_SUBROUTINE