[modeller_usage] structure not read in

[sankari thirumal <>]

Hi modeller,

 

My protein sequence is aligned with the template sequence. I've done the alignment according to the psipred alignment. Hence i have to delete the first 40 residues in my protein seq to be modeled and 16 residues in the template sequence.

 

The actual length of my sequence is 500
The actual lenth of template is 455

 

I have the following quries

 

I have aligned the file in clustal and i'm getting only .aln file (in the pir format)  and not .ali file

 

Please tell me whether am i right?

 

I have downloaded the pdb file and placed in the atom files folder.
I have aligned the sequences as i said earlier and ranamed the file as apnew.ali put it in the automodel directory.
I have also modified the model-defalut.py file and named as model-template.py

 

Now my question is when i place the template file with full 455 residues, while  40 residues deleted in  the alignment will it create some problems?

 

and also tell me

 

How to get the .ali file?

This is the error message i recieve when i run the modeller,  what to do can anyone help?

 

C:\Program Files\Modeller8v1\examples\automodel>mod8v1 model-template.py
Traceback (most recent call last):
  File "model-template.py", line 18, in ?
    a.make()                            # do the actual homology modelling
  File "C:\Program Files\Modeller8v1\modlib\modeller\automodel\automodel.py", li
ne 100, in make
    self.homcsr(exit_stage)
  File "C:\Program Files\Modeller8v1\modlib\modeller\automodel\automodel.py", li
ne 331, in homcsr
    aln.check()
  File "C:\Program Files\Modeller8v1\modlib\modeller\alignment.py", line 153, in
 check
    io=io.modpt, libs=libs.modpt, **vars)
  File "C:\Program Files\Modeller8v1\modlib\modeller\util\top.py", line 37, in c
heck_alignment
    return _modeller.check_alignment(aln, io, libs, *args)
_modeller.error: check_a_337E> Structure not read in:        1

 

C:\Program Files\Modeller8v1\examples\automodel>

 

 

regards

 

san

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# Homology modelling by the automodel class

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  = 'Apnew.ali',     # alignment filename
              knowns   = '1u13',              # codes of the templates
              sequence = '1ptg')              # 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

Attachment: Apnew.ali
Description: 903132944-Apnew.ali

Attachment: model-template.log
Description: 3063897076-model-template.log