Hi all, suppose I have the following simple "dummy" py-modeller script:
from modeller import * from modeller.automodel import * log.verbose() env = environ()
env.io.atom_files_directory = '<path to pdb>' # containing d1f0la3.pdb a = automodel(env, alnfile = '<my_pir_file.pir>', # alignment filename knowns = 'd1f0la3', # codes of the templates sequence ='d1f0la3') # code of the target a.starting_model = 1 a.ending_model = 3 a.make()
and the corresponding pir file: >P1;d1f0la3 sequence:d1f0la3: 1: : 180: :f.1.2.1 (A;201-380) Diphtheria toxin, middle domain {Corynebacterium diphtheriae [TaxId; 1717]} PDB; d1ddta3 d1p3gb_ d1p3gf_ d1p3pb_ d1p3pf_ d1p3bf_ d1p3ib_: : 0.00: 0.00 CINLDWDVIRDKTKTKIESLKEHGPIKNKMSESPNKTVSEEKAKQYLEEFHQTALEHPELSELKTVTGTNPVFAGANYAAWAVNVAQVIDSETADNLEKT TAALSILPGIGSVMGIADGAVHHNTEEIVAQSIALSSLMVAQAIPLVGELVDIGFAAYNFVESIINLFQVVHNSYNRPAY* >P1;d1f0la3 structureX:d1f0la3: :A: :A:f.1.2.1 (A201-380) Diphtheria toxin, middle domain {Corynebacterium diphtheriae [TaxId 1717]} PDB d1ddta3 d1p3gb_ d1p3gf_ d1p3pb_ d1p3pf_ d1p3bf_ d1p3ib_:Corynebacterium diphtheriae [TaxId; 1717]:-1.00:-1.00 CINLDWDVIRDKTKTKIESLKEHGPIKNKMSESPNKTVSEEKAKQYLEEFHQTALEHPELSELKTVTGTNPVFAGANYAAWAVNVAQVIDSETADNLEKT TAALSILPGIGSVMGIADGAVHHNTEEIVAQSIALSSLMVAQAIPLVGEL--IGFAAYNFVESIINLFQVVHNSYNRPAY*
Then I get the following error when executing the script: Traceback (most recent call last): File "/cluster/tmp/armin/test/d1f0la3_d1f0la3_1.py", line 14, in <module> a.make() File "/cluster/bioprogs/modeller9v5_RSR/modlib/modeller/automodel/automodel.py", line 98, in make self.homcsr(exit_stage) File "/cluster/bioprogs/modeller9v5_RSR/modlib/modeller/automodel/automodel.py", line 425, in homcsr self.check_alignment(aln) File "/cluster/bioprogs/modeller9v5_RSR/modlib/modeller/automodel/automodel.py", line 407, in check_alignment aln.check() File "/cluster/bioprogs/modeller9v5_RSR/modlib/modeller/alignment.py", line 191, in check self.check_structure_structure(io=io) File "/cluster/bioprogs/modeller9v5_RSR/modlib/modeller/alignment.py", line 200, in check_structure_structure return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst)
_modeller.ModellerError: check_a_282E> Unable to read structural information for alignment sequence: 1 d1f0la3 This command requires structures.
Any ideas whats wrong? Thanks in advance Armin