Re: [modeller_usage] Error in 8v2

[Dhananjay <dhananjay.c.joshi@gmail.com>]

Hello all,

thanks for reply for last problem.

Still  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


Let me tell you what I have done yet. 

I made a directory containing template and target fasta files. Then I aligned it using clustaW online. 

Using the alignment I formed a alignment.ali file. 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. 

Why it can't read the structure file ?  

do I need to form a .atm file or is there anything wrong in my steps......




 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/
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Dhananjay C Joshi
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