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.
Torsten Stauder wrote: > 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
That's odd - there should be a more descriptive error message in the log file. If you can send me your input files (alignment_final.ali, and the PDB file you're using for a627) then I can take a look.
> 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?
You only need the sequence, in a PIR file.
Ben Webb, Modeller Caretaker
Torsten Stauder wrote: > 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
When I run your input files with mod8v2, my log file says:
runcmd______> alignment.check()
check_a_343_> >> BEGINNING OF COMMAND openf5__224_> Open 11 OLD SEQUENTIAL ./pdb1rjb.ent rdpdb___303E> No atoms were read from the specified input PDB file, since the starting residue number and/or chain id in MODEL_SEGMENT (or the alignment file header) was not found; requested starting position: residue number " 572", chain " " rdabrk__288W> Protein not accepted: 1 1rjb check_a_337E> Structure not read in (please consult the log file for more details): 1 1rjb
I don't know why you're not seeing this in your own log file. But what this error means is that alignment is telling Modeller to read from residue number 572 in the ' ' chain (i.e. no ID). But the first chain in 1rjb is the 'A' chain. So you need to modify your alignment file header to read >P1;1rjb structureX:1rjb:572 :A:947 :A:FLT3 wt: : :
or similar.
Ben Webb, Modeller Caretaker