Dear Modeller team,
I'm trying to get the format right for a multiple alignment, I did in HHpred server to use as input to modeller. I don't understand the error messages. I don't know if the errors are related to the PDB file since I have not changed anything in original PDB unless the extension. I would appreciate very much your advice.
Thanks in advance for your help! Maryam
***The input python script: # Comparative modeling by the automodel class from modeller import * # Load standard Modeller classes 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 = 'XPF_nuc.ali', # alignment filename knowns = '1j23','4bxo', # codes of the templates sequence = 'XPF') # 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 comparative modeling
***The run command: mod9.11 model_test1.py
***atom_files: $ ls -l total 952 -rw-r--r-- 1 mfaridou users 121905 Aug 25 23:07 1j23.atm -rw-r--r-- 1 mfaridou users 121905 Aug 25 23:08 1j23.pdb -rw-r--r-- 1 mfaridou users 362313 Aug 25 23:08 4bxo.atm -rw-r--r-- 1 mfaridou users 362313 Aug 25 23:08 4bxo.pdb
*** input file XPF_nuc.ali >P1;1j23 structurex:1j23:5:A:125:A:HEFnuclease:Pyrococcus furiosus:1.78:0.248 QEGVKVVVDSRELRSEVVKRLKLLGVKLEVKTLDVGDYIISEDVAIERKSANDLIQSIIDGGLFDQVKRLKEAYSRPIMIVEGS-LY---------GIRNVHPNAIRGAIAAVTVDF-GVPIIFSSTPEETAQYI*
>P1;4bxo structurex:4bxo:1:A:151:A:FANCMprotein:Homo sapiens:2.15:0.255 GSGSRPHLAGTHTSLRLPQEGKGTCILVGGHEITSGLEVISSLRAIHGLQVEVCPLNGCDYIVSNRMVVERRSQSEMLNSVNKNKFIEQIQHLQSMFERICVIVEKDREKTGD------TSRMFRRTKSYDSLLTTLIGA-GIRILFSSCQEETADLL*
>P1;XPF sequence:XPF:.:.:156:.::0.00: 0.00 RGTASADVSTDTRKAGGQEQNGTQQSIVVDMREFRSELPSLIHRRGIDIEPVTLEVGDYILTPEMCVERKSISDLIGSLNNGRLYSQCISMSRYYKRPVLLIEFDPSKPFSLTSRGALFQEISSNDISSKLTLLTLHFPRLRILWCPSPHATAELF*
***The runtime messages: 'import site' failed; use -v for traceback Traceback (most recent call last): File "model_test1.py", line 18, in ? a.make() # do the actual comparative modeling File "/home/software/software//modeller_v9.11/modlib/modeller/automodel/automodel.py", line 96, in make self.homcsr(exit_stage) File "/home/software/software//modeller_v9.11/modlib/modeller/automodel/automodel.py", line 423, in homcsr self.check_alignment(aln) File "/home/software/software//modeller_v9.11/modlib/modeller/automodel/automodel.py", line 405, in check_alignment aln.check() File "/home/software/software//modeller_v9.11/modlib/modeller/alignment.py", line 197, in check self.check_structure_structure(io=io) File "/home/software/software//modeller_v9.11/modlib/modeller/alignment.py", line 206, in check_structure_structure return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst) _modeller.SequenceMismatchError: read_te_291E> Sequence difference between alignment and pdb :
On 8/26/16 1:58 PM, Maryam Faridounnia wrote: > I'm trying to get the format right for a multiple alignment, I did in > HHpred server to use as input to modeller. I don't understand the error > messages.
I only see one error message:
> _modeller.SequenceMismatchError: read_te_291E> Sequence difference > between alignment and pdb :
I'm not sure how to state the error any more clearly than it is already... but the sequence in your alignment has to match the sequence in the PDB file. So you have to change one or the other (usually the alignment) so that they match. If you look in the Modeller log file it will show you exactly where the mismatch occurred. Usually it's just a single residue mutation or a short insertion.
Ben Webb, Modeller Caretaker
So, none of the other lines are not errors.
I meant to put all the errors, while running other commands, but found it too long. With this one, I checked one log file and it was empty. I will check another when I have access.
Thanks
On Fri, Aug 26, 2016 at 6:03 PM, Modeller Caretaker < modeller-care@salilab.org> wrote:
> On 8/26/16 1:58 PM, Maryam Faridounnia wrote: > >> I'm trying to get the format right for a multiple alignment, I did in >> HHpred server to use as input to modeller. I don't understand the error >> messages. >> > > I only see one error message: > > _modeller.SequenceMismatchError: read_te_291E> Sequence difference >> between alignment and pdb : >> > > I'm not sure how to state the error any more clearly than it is already... > but the sequence in your alignment has to match the sequence in the PDB > file. So you have to change one or the other (usually the alignment) so > that they match. If you look in the Modeller log file it will show you > exactly where the mismatch occurred. Usually it's just a single residue > mutation or a short insertion. > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org https://salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage >
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Maryam Faridounnia -
Modeller Caretaker