Error when reading the alignment PIR file.
Hi,
Please help me if possible, I have been stuck few days by now :-(
I am trying a very basic approach to use modeller, but in this case I am using my own global alignment from clustalW. I am trying a very basic protein, target: 1aho, and only one template 2kbh_A
ClustalW outputs the alignment in PIR format ( http://www.bioinformatics.nl/tools/crab_pir.html) but is a different PIR format than the one required by modeller. Actually the main difference is that clustalW does not provide the *start residue*:*start chain code*:*endresidue :end chain code: parts.*
I do not know how to get that information and modeller apparently does not know either. Here I copy and paste the clustalW PIR format, the PIR modeller format and the errors I get from the model_simple.log.
*CLUSTALW PIR format - sequencealn.pir*
>P1;1AHO_A|PDBID|CHAIN|SEQUENCE
VKDGYIVDDVNCTYFCGRNAYCNEECTKLKGESGYCQWASPYGNACYCYK LPDHVRTKGPGRCH-- * >P1;2KBH_A|PDBID|CHAIN|SEQUENCE
VKDGYIADDRNCPYFCGRNAYCDGECKKNRAESGYCQWASKYGNACWCYK LPDDARIMKPGRCNGG *
*MODELLER INPUT (does not work, not sure why)*
>P1;1aho sequence:1aho: : : : ::: 0.00: 0.0 VKDGYIVDDVNCTYFCGRNAYCNEECTKLKGESGYCQWASPYGNACYCYK LPDHVRTKGPGRCH--*
>P1;2kbhA structureX:2kbh.pdb: : : : ::: 0.00: 0.0 VKDGYIADDRNCPYFCGRNAYCDGECKKNRAESGYCQWASKYGNACWCYK LPDDARIMKPGRCNGG*
*ERROR MODELLER GIVES ME:*
get_ran_648E> Alignment sequence not found in PDB file: 1 2kbh.pdb (You didn't specify the starting and ending residue numbers and chain IDs in the alignment, so Modeller tried to guess these fr the PDB file.) Suggestion: put in the residue numbers and chain IDs (see the manual) and run again for more detailed diagnostics. You could also try running with allow_alternates=True to accept alternate one-letter code matches (e.g. B to N, Z to Q). Traceback (most recent call last): File "hoModeller-clustalaln.py", line 14, in <module> a.make() # do the homollogy modelling File "/n/sw/modeller-9v7/modlib/modeller/automodel/automodel.py", line 98, self.homcsr(exit_stage) File "/n/sw/modeller-9v7/modlib/modeller/automodel/automodel.py", line 411, aln = self.read_alignment() File "/n/sw/modeller-9v7/modlib/modeller/automodel/automodel.py", line 401, aln.append(file=self.alnfile, align_codes=self.knowns+[self.sequence]) File "/n/sw/modeller-9v7/modlib/modeller/alignment.py", line 79, in append allow_alternates) _modeller.SequenceMismatchError: get_ran_648E> Alignment sequence not found i
I am aware that the error advice me to put the start and ending residues numbers but I am still not sure how to solve the issue.
Any help will be strongly appreciated, I need to use modeller as soon as possible to do some progress in my research.
Best,
You need to specify which part of the sequence of your template you are using. Not specifying it causes the error message "Alignment sequence not found in PDB file...". You can find more information about the alignment format here: http://salilab.org/modeller/manual/node445.html#alignmentformat Also, your template seems to be a NMR structure, you need to replace the structureX with NMR.
Try using these sequences in your alignment file:
P1;1aho sequence:1aho:FIRST:@ END:::::: VKDGYIVDDVNCTYFCGRNAYCNEECTKLKGESGYCQWASPYGNACYCYK LPDHVRTKGPGRCH--*
P1;2kbhA NMR:2kbh.pdb:FIRST:@ END:::::: VKDGYIADDRNCPYFCGRNAYCDGECKKNRAESGYCQWASKYGNACWCYK LPDDARIMKPGRCNGG*
On Mon, Apr 12, 2010 at 08:08, Daniel Fernandez dfernan@gmail.com wrote: > Hi, > Please help me if possible, I have been stuck few days by now :-( > I am trying a very basic approach to use modeller, but in this case I am > using my own global alignment from clustalW. I am trying a very basic > protein, target: 1aho, and only one template 2kbh_A > ClustalW outputs the alignment in PIR format > (http://www.bioinformatics.nl/tools/crab_pir.html) but is a different PIR > format than the one required by modeller. Actually the main difference is > that clustalW does not provide the start residue:start chain code:end > residue:end chain code: parts. > I do not know how to get that information and modeller apparently does not > know either. Here I copy and paste the clustalW PIR format, the PIR modeller > format and the errors I get from the model_simple.log. > CLUSTALW PIR format - sequencealn.pir >>P1;1AHO_A|PDBID|CHAIN|SEQUENCE > VKDGYIVDDVNCTYFCGRNAYCNEECTKLKGESGYCQWASPYGNACYCYK > LPDHVRTKGPGRCH-- > * >>P1;2KBH_A|PDBID|CHAIN|SEQUENCE > VKDGYIADDRNCPYFCGRNAYCDGECKKNRAESGYCQWASKYGNACWCYK > LPDDARIMKPGRCNGG > * > MODELLER INPUT (does not work, not sure why) >>P1;1aho > sequence:1aho: : : : ::: 0.00: 0.0 > VKDGYIVDDVNCTYFCGRNAYCNEECTKLKGESGYCQWASPYGNACYCYK > LPDHVRTKGPGRCH--* >>P1;2kbhA > structureX:2kbh.pdb: : : : ::: 0.00: 0.0 > VKDGYIADDRNCPYFCGRNAYCDGECKKNRAESGYCQWASKYGNACWCYK > LPDDARIMKPGRCNGG* > ERROR MODELLER GIVES ME: > get_ran_648E> Alignment sequence not found in PDB file: 1 2kbh.pdb > (You didn't specify the starting and ending residue numbers > and > chain IDs in the alignment, so Modeller tried to guess these > fr > the PDB file.) > Suggestion: put in the residue numbers and chain IDs (see the > manual) and run again for more detailed diagnostics. > You could also try running with allow_alternates=True to > accept > alternate one-letter code matches (e.g. B to N, Z to Q). > Traceback (most recent call last): > File "hoModeller-clustalaln.py", line 14, in <module> > a.make() # do the homollogy modelling > File "/n/sw/modeller-9v7/modlib/modeller/automodel/automodel.py", line 98, > self.homcsr(exit_stage) > File "/n/sw/modeller-9v7/modlib/modeller/automodel/automodel.py", line > 411, > aln = self.read_alignment() > File "/n/sw/modeller-9v7/modlib/modeller/automodel/automodel.py", line > 401, > aln.append(file=self.alnfile, align_codes=self.knowns+[self.sequence]) > File "/n/sw/modeller-9v7/modlib/modeller/alignment.py", line 79, in append > allow_alternates) > _modeller.SequenceMismatchError: get_ran_648E> Alignment sequence not found > i > I am aware that the error advice me to put the start and ending residues > numbers but I am still not sure how to solve the issue. > Any help will be strongly appreciated, I need to use modeller as soon as > possible to do some progress in my research. > Best, > -- > Daniel F. > > Department of Statistics, Harvard University > 1 Oxford Street, Cambridge, MA 02138 > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > >
Hi all,
Thanks you very much for such a prompt response! :-)
Working now!
Summary of successfully produced models: Filename molpdf DOPE score GA341 score ---------------------------------------------------------------------- 1aho.B99990001.pdb 424.19452 -5177.44580 1.00000 1aho.B99990002.pdb 408.62314 -5174.39111 1.00000 1aho.B99990003.pdb 378.08508 -5317.75439 1.00000 1aho.B99990004.pdb 362.42450 -5208.25195 1.00000 1aho.B99990005.pdb 398.92511 -5020.92676 1.00000
:-) :-)
On Mon, Apr 12, 2010 at 4:07 AM, Thomas Juettemann juettemann@gmail.comwrote:
> You need to specify which part of the sequence of your template you > are using. Not specifying it causes the error message "Alignment > sequence not found in PDB file...". > You can find more information about the alignment format here: > http://salilab.org/modeller/manual/node445.html#alignmentformat > Also, your template seems to be a NMR structure, you need to replace > the structureX with NMR. > > Try using these sequences in your alignment file: > > P1;1aho > sequence:1aho:FIRST:@ END:::::: > VKDGYIVDDVNCTYFCGRNAYCNEECTKLKGESGYCQWASPYGNACYCYK > LPDHVRTKGPGRCH--* > > P1;2kbhA > NMR:2kbh.pdb:FIRST:@ END:::::: > VKDGYIADDRNCPYFCGRNAYCDGECKKNRAESGYCQWASKYGNACWCYK > LPDDARIMKPGRCNGG* > > > > On Mon, Apr 12, 2010 at 08:08, Daniel Fernandez dfernan@gmail.com wrote: > > Hi, > > Please help me if possible, I have been stuck few days by now :-( > > I am trying a very basic approach to use modeller, but in this case I am > > using my own global alignment from clustalW. I am trying a very basic > > protein, target: 1aho, and only one template 2kbh_A > > ClustalW outputs the alignment in PIR format > > (http://www.bioinformatics.nl/tools/crab_pir.html) but is a different > PIR > > format than the one required by modeller. Actually the main difference > is > > that clustalW does not provide the start residue:start chain code:end > > residue:end chain code: parts. > > I do not know how to get that information and modeller apparently does > not > > know either. Here I copy and paste the clustalW PIR format, the PIR > modeller > > format and the errors I get from the model_simple.log. > > CLUSTALW PIR format - sequencealn.pir > >>P1;1AHO_A|PDBID|CHAIN|SEQUENCE > > VKDGYIVDDVNCTYFCGRNAYCNEECTKLKGESGYCQWASPYGNACYCYK > > LPDHVRTKGPGRCH-- > > * > >>P1;2KBH_A|PDBID|CHAIN|SEQUENCE > > VKDGYIADDRNCPYFCGRNAYCDGECKKNRAESGYCQWASKYGNACWCYK > > LPDDARIMKPGRCNGG > > * > > MODELLER INPUT (does not work, not sure why) > >>P1;1aho > > sequence:1aho: : : : ::: 0.00: 0.0 > > VKDGYIVDDVNCTYFCGRNAYCNEECTKLKGESGYCQWASPYGNACYCYK > > LPDHVRTKGPGRCH--* > >>P1;2kbhA > > structureX:2kbh.pdb: : : : ::: 0.00: 0.0 > > VKDGYIADDRNCPYFCGRNAYCDGECKKNRAESGYCQWASKYGNACWCYK > > LPDDARIMKPGRCNGG* > > ERROR MODELLER GIVES ME: > > get_ran_648E> Alignment sequence not found in PDB file: 1 > 2kbh.pdb > > (You didn't specify the starting and ending residue numbers > > and > > chain IDs in the alignment, so Modeller tried to guess > these > > fr > > the PDB file.) > > Suggestion: put in the residue numbers and chain IDs (see > the > > manual) and run again for more detailed diagnostics. > > You could also try running with allow_alternates=True to > > accept > > alternate one-letter code matches (e.g. B to N, Z to Q). > > Traceback (most recent call last): > > File "hoModeller-clustalaln.py", line 14, in <module> > > a.make() # do the homollogy modelling > > File "/n/sw/modeller-9v7/modlib/modeller/automodel/automodel.py", line > 98, > > self.homcsr(exit_stage) > > File "/n/sw/modeller-9v7/modlib/modeller/automodel/automodel.py", line > > 411, > > aln = self.read_alignment() > > File "/n/sw/modeller-9v7/modlib/modeller/automodel/automodel.py", line > > 401, > > aln.append(file=self.alnfile, > align_codes=self.knowns+[self.sequence]) > > File "/n/sw/modeller-9v7/modlib/modeller/alignment.py", line 79, in > append > > allow_alternates) > > _modeller.SequenceMismatchError: get_ran_648E> Alignment sequence not > found > > i > > I am aware that the error advice me to put the start and ending residues > > numbers but I am still not sure how to solve the issue. > > Any help will be strongly appreciated, I need to use modeller as soon as > > possible to do some progress in my research. > > Best, > > -- > > Daniel F. > > > > Department of Statistics, Harvard University > > 1 Oxford Street, Cambridge, MA 02138 > > > > _______________________________________________ > > modeller_usage mailing list > > modeller_usage@salilab.org > > https://salilab.org/mailman/listinfo/modeller_usage > > > > >
On 04/12/2010 01:07 AM, Thomas Juettemann wrote: > Also, your template seems to be a NMR structure, you need to replace > the structureX with NMR.
Well, that's just cosmetic - it won't affect generation of models. But Modeller does not understand "NMR" (so it will fall back to the default, "structureX"). For NMR structures, use "structureN" in your alignment file.
Ben Webb, Modeller Caretaker
participants (3)
-
Daniel Fernandez -
Modeller Caretaker -
Thomas Juettemann