I had to do an automodelling of a protein based on a template.
I first ran the seqcheck and use the sequences that I got for the alignment (using tcoffee).
I prepared the alignment file as follow:
>P1;1GNS sequence:1GNS: 4 :A: 275 :A:undefined:undefined:-1.00:-1.00 GPYGVSQIKAP-ALHSQGYTGSNVKVAVIDSGID------SSHPALKVAGGASFVPSETN PFQDNNSHGTHVAGTVLA-------VAPSASLYAVKVLGADGS--GQYSWIINGIEWAIA NNMDVINMSLGGPSGSAALKAA---VDKAVASGVVVVAAAGNEGTSGSSSTVGYPGKYPS VIAVGAV-----------DSSNQRASFSSVGP------ELDVMAPGVSIWSTL------- -----PGNKYGAKSGT-MASPHVAGAAALI------------------------------ -------------LSKHPNWTNTQVRSSLE------------------------------ -----------------NTTTKLGDSFYYG--------------------KGLINVEAAA ---------------Q* >P1;1WMD structureX:1WMD: 1 :A: 434 :A:undefined:undefined:-1.00:-1.00 NDVARGIVKADVAQSSYGLYGQGQIVAVADTGLDTGRNDSSMHEAFRGKITALYALGRTN NANDTNGHGTHVAGSVLGNGSTNKGMAPQANLVFQSIMDSGGGLGGLPSNLQTLFSQAYS AGARIHTNSWGAAVNGAYTTDSRNVDDYVRKNDMTILFAAGNEGPNGG--TISAPGTAKN AITVGATENLRPSFGSYADNINHVAQFSSRGPTKDGRIKPDVMAPGTFILSARSSLAPDS SFWANHDSKYAYMGGTSMATPIVAGNVAQLREHFVKNRGITPKPSLLKAALIAGAADIGL GYPNGNQGWGRVTLDKSLNVAYVNESSSLSTSQKATYSFTATAGKPLKISLVWSDAPAST TASVTLVNDLDLVITAPNGTQYVGNDFTSPYNDNWDGRNNVENVFINAPQSGTYTIEVQA YNVPVGPQTFSLAIVN*
this is my script for the automodelling:
# Homology modelling by the automodel class
from modeller.automodel import * # Load the automodel class
log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in
# directories for input atom files
env.io.atom_files_directory = './:../home/Bis/gbastian/Documents/Data/ExcerciseModeling/SUBTILISIN BPN/Structure files/'
a = automodel(env, alnfile = 'alignedsequences.ali', # alignment filename knowns = '1WMD', # codes of the templates sequence = '1GNS') # code of the target
a.starting_model= 1 # index of the first model a.ending_model = 10 # index of the last model
# (determines how many models to calculate) a.make() # do the actual homology modelling
and this is what I got after running it:
openf5__224_> Open 11 OLD SEQUENTIAL $(LIB)/restyp.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/resdih.lib rdrdih__263_> Number of dihedral angle types : 9 Maximal number of dihedral angle optima: 3 Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/radii.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/radii14.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/mnch1.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/mnch2.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/mnch3.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/xs4.mat rdrrwgh_268_> Number of residue types: 21 runcmd______> alignment.append(align_codes=['1WMD', '1GNS'], atom_files=[], file='alignedsequences.ali', (def)remove_gaps=True, (def)alignment_format='PIR', add_sequence=True, (def)rewind_file=False, (def)close_file=True)
openf___224_> Open alignedsequences.ali
Dynamically allocated memory at amaxalignment [B,kB,MB]: 2270569 2217.353 2.165
Dynamically allocated memory at amaxalignment [B,kB,MB]: 2293501 2239.747 2.187
Dynamically allocated memory at amaxalignment [B,kB,MB]: 2316901 2262.599 2.210
Dynamically allocated memory at amaxalignment [B,kB,MB]: 2363701 2308.302 2.254
Dynamically allocated memory at amaxalignment [B,kB,MB]: 2457301 2399.708 2.343
Dynamically allocated memory at amaxalignment [B,kB,MB]: 2644501 2582.521 2.522
Read the alignment from file : alignedsequences.ali Total number of alignment positions: 436
# Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1WMD 434 1 1WMD undefined 2 1GNS 262 1 1GNS undefined runcmd______> alignment.check()
check_a_343_> >> BEGINNING OF COMMAND pdbnam__217W> Filename for PDB code not found: 1WMD Directories: ./:../home/Bis/gbastian/Documents/Data/ExcerciseModeling/SUBTILISIN BPN/Structure files/ Extensions : :.atm:.pdb:.ent:.crd rdabrk__288W> Protein not accepted: 1 1WMD check_a_337E> Structure not read in (please consult the log file for more details): 1 1WMD
What's wrong with my PDB??
I checked the name reference and they are all right.
Thanks a lot
Giacomo