[modeller_usage] Modeling Multidomain proteins

-- 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