Hi modellers,
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 queries
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
I have attached the log file, ali file and also the modified
model-default.py file
Thanks in advance
sankari
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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
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