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
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
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?