Hello all,
I am getting followin error while running mod8v2 model-default.py
[dhananjay@cdfd-wstn7 automodel] mod8v2 model-default.py Traceback (most recent call last): File "model-default.py", line 18, in ? a.make() # do the actual homology modelling File "/users/dhananjay/bin/modeller8v2/modlib/modeller/automodel/automodel.py", line 100, in make self.homcsr(exit_stage) File "/users/dhananjay/bin/modeller8v2/modlib/modeller/automodel/automodel.py", line 318, in homcsr aln = self.read_alignment() File "/users/dhananjay/bin/modeller8v2/modlib/modeller/automodel/automodel.py", line 312, in read_alignment aln.append(file=self.alnfile, align_codes=self.knowns+[self.sequence]) File "/users/dhananjay/bin/modeller8v2/modlib/modeller/alignment.py", line 36, in append return self.__int_append('alignment.append', io, libs, vars) File "/users/dhananjay/bin/modeller8v2/modlib/modeller/alignment.py", line 68, in __int_append libs=libs.modpt, **vars) File "/users/dhananjay/bin/modeller8v2/modlib/modeller/util/top.py", line 33, in read_alignment return _modeller.read_alignment(aln, io, libs, *args)
_modeller.error: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1) = 1M1G
I am new to this software. Please tell me whats wrong here
Thanking you in advance
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 wrote: > > Hello all, > > I am getting followin error while running mod8v2 model-default.py > > > > > [dhananjay@cdfd-wstn7 automodel] mod8v2 model-default.py > Traceback (most recent call last): > File "model-default.py ", line 18, in ? > a.make() # do the actual homology modelling > File > "/users/dhananjay/bin/modeller8v2/modlib/modeller/automodel/automodel.py", > line 100, in make > self.homcsr (exit_stage) > File > "/users/dhananjay/bin/modeller8v2/modlib/modeller/automodel/automodel.py", > line 318, in homcsr > aln = self.read_alignment() > File > "/users/dhananjay/bin/modeller8v2/modlib/modeller/automodel/automodel.py", > line 312, in read_alignment > aln.append(file=self.alnfile, align_codes=self.knowns+[self.sequence]) > File "/users/dhananjay/bin/modeller8v2/modlib/modeller/alignment.py", > line 36, in append > return self.__int_append('alignment.append ', io, libs, vars) > File "/users/dhananjay/bin/modeller8v2/modlib/modeller/alignment.py", > line 68, in __int_append > libs=libs.modpt, **vars) > File "/users/dhananjay/bin/modeller8v2/modlib/modeller/util/top.py", > line 33, in read_alignment > return _modeller.read_alignment(aln, io, libs, *args) > > > _modeller.error: read_al_373E> Protein specified in ALIGN_CODES(i) was not > found in the alignment file; ALIGN_CODES( 1) = 1M1G > > > > I am new to this software. Please tell me whats wrong here > > > 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 > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > > >
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
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/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage >
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 > -- > modeller-care@salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage >
Dhananjay wrote: > 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
Check the 1g7s PDB file. Like the log file says, it didn't read in the sequence because your alignment says to start from residue 1 in chain A, and it couldn't find that in the PDB file.
Ben Webb, Modeller Caretaker
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Dhananjay -
Modeller Caretaker -
sako biochem