Hi mailing list!

I'm new to "modeller" and actually my modelling doesn't work. However... let my explain...

Given is a tyrosine kinase, whose structure is already known. In some cases, this tyrosine kinase is mutated and a so called "internal tandem duplication" [itd] is inserted.

It looks like this:

wild type sequence: AAAAAAAAAAAAABBBBBBBBBBBBBBB

itd: AAAAAAAAAAAAAxxxxxxxxxxxBBBBBBBBBBBBBBB (x = insertion)

So I have been performing an alignment and tried to run it with modeller. "model-default.py" was used for the first test.

Here is, what the logfile "says":

Kind, OS, HostName, Kernel, Processor: 4, Linux audio 2.6.15.1 i686 Date and time of compilation : 02/28/2006 18:03:39 MODELLER executable type : i386-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2006/07/10 18:27:11.105

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=['a627', '1rjb'], atom_files=[], file='alignment_final.ali', (def)remove_gaps=True, (def)alignment_format='PIR', add_sequence=True, (def)rewind_file=False, (def)close_file=True)

openf___224_> Open alignment_final.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 : alignment_final.ali Total number of alignment positions: 426

# Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 a627 426 1 a627 FLT3 mutated ITD 2 1rjb 344 1 1rjb FLT3 wild type runcmd______> alignment.check()

check_a_343_> >> BEGINNING OF COMMAND check_a_337E> Structure not read in (please consult the log file for more details): 1 a627

This is my modified "model-default.py"

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 = './:../atom_files'

a = automodel(env, alnfile = 'alignment_final.ali', # alignment filename knowns = 'a627', # codes of the templates sequence = '1rjb') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model # (determines how many models to calculate) a.make() # do the actual homology modelling

Any hints? Why has the structure not read? Another question: Do I have to provide my sequence to be modelled a .pdb-file using "0.00" as coordinates or is it sufficient to provide it as .fasta?

Thanks in advance.