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
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
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
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