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
--
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Dhananjay C Joshi
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