Hello all,
thanks for reply for last problem.
I am getting the error as follows:
[dhananjay@cdfd-grid-node2 modeller_nusG] mod8v2 script 'import site' failed; use -v for traceback Traceback (most recent call last): File "script", line 18, in ? a.make() # do the actual homology modelling File "/users/dhananjay/Dhananjay_installation/modeller-8v2_linux/modlib/modeller/automodel/automodel.py", line 100, in make self.homcsr(exit_stage) File "/users/dhananjay/Dhananjay_installation/modeller-8v2_linux/modlib/modeller/automodel/automodel.py", line 331, in homcsr aln.check() File "/users/dhananjay/Dhananjay_installation/modeller-8v2_linux/modlib/modeller/alignment.py", line 153, in check io=io.modpt, libs=libs.modpt, **vars) File "/users/dhananjay/Dhananjay_installation/modeller-8v2_linux/modlib/modeller/util/top.py", line 37, in check_alignment return _modeller.check_alignment(aln, io, libs, *args) _modeller.error: check_a_337E> Structure not read in (please consult the log file for more details): 1 1M1G
Part of model-default.log file is as follows:
Read the alignment from file : alignment.ali Total number of alignment positions: 610
# Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1g7s 594 1 1g7s Initiation factop 2 NIF 595 1 NIF runcmd______> alignment.check()
check_a_343_> >> BEGINNING OF COMMAND openf5__224_> Open 11 OLD SEQUENTIAL 1g7s 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 " 1", chain " A" rdabrk__288W> Protein not accepted: 1 1g7s check_a_337E> Structure not read in (please consult the log file for more details): 1 1g7s "script.log" 77L, 4310C
Let me tell you what I have done yet.
I made a directory containing template (taken from NCBI blast output) and target fasta files. Then I aligned it using clustaW online.
Using the alignment, I formed a alignment.ali file. Here I have just copied the aligned sequences, as it is, in the alignment.ali file and edited as per the format given on web.
Then I have copied model-default.py to the same folder and made the changes as per the requirement, like alignment filename, codes of the templates, code of the target and env.io.atom_files_directory = the directory where I put all the above files.
Using this script I typed the command: mod8v2 model-default.py And then I got this error.
>From the above message it seems that the pdb file residues and the corresponding sequence taken from the web are not matching , i.e. starting residue are not present in .pdb file .
>From BLAST output, the templates that I have chosen have more no. of residues than that of in .pdb file of the same remplate.
Do I need to form .PIR file from the template .pdb file (chosen throu BLAST) and then go for modeling task ?
If so then any specific programm for converting .pdb to .PIR format ?
Thanking you in advance,
On 11/22/06, Modeller Caretaker modeller-care@salilab.org wrote: > > sako biochem wrote: > > your pdb file name that you write in your alignment file is not equal > > with your pdb file in atom file folder. > > > > On 22/11/06, *Dhananjay* <dhananjay.c.joshi@gmail.com > > mailto:dhananjay.c.joshi@gmail.com> wrote: > ... > > _modeller.error: read_al_373E> Protein specified in ALIGN_CODES(i) > > was not found in the alignment file; ALIGN_CODES( 1) = 1M1G > > No, this means that the code specified in the Python script ('1M1G') is > not in the alignment file. This may be because you mistyped the code of > the protein, misunderstood the PIR file format, or mixed upper and lower > case (Modeller is case sensitive). It hasn't got as far as trying to > read the PDB file at this point. > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage >