[modeller_usage] Modeling Multidomain proteins

[Tjaart de Beer <>]

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:  
	

>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