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Re: [modeller_usage] Error in 8v2
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,
--
Dhananjay C Joshi
Project Assistant
LT & LSB, C D F D
ECIL Road, Nacharam
Hyderabad-500 076, INDIA
Tel : +91-40-27151344
Fax : +91-40-27155610