[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

[modeller_usage] query



Hi..

I am doing advance modelling with multiple template . I have to add ATP ang Mg in my structure . I am trying to add @ , $ for the purpose ,ATP hetero atom is present in the template even though its giving error .

Can I add ATP in 1 of the template only .

The error is - 
File "model_mult.py", line 9, in ?
    a.make()
  File "/nfs/condor/home/ajeeta/bin/modeller9v1/modlib/modeller/automodel/automodel.py", line 108, in make
    self.homcsr(exit_stage)
  File "/nfs/condor/home/ajeeta/bin/modeller9v1/modlib/modeller/automodel/automodel.py", line 416, in homcsr
    aln.check()
  File "/nfs/condor/home/ajeeta/bin/modeller9v1/modlib/modeller/alignment.py", line 154, in check
    libs=self.env.libs.modpt)
_modeller.error: rdabrk__337E> Structure not read in...

The log file is -

runcmd______> alignment.append(align_codes=['2FFAA', '1XEFA', '2FFBA', 'CaNBD'], atom_files=[], file='CaNBD-mult.ali', (def)remove_gaps=True, (def)alignment_format='PIR', (def)rewind_file=False, (def)close_file=True)
read_te_290E> Number of residues in the alignment and  pdb files are different:      242      241
              For alignment entry:        2  1XEFA
                                 x  (mismatch at alignment position    242)
 Alignment   KELLSEPESLYSYLYQLQSD@                                       
       PDB   KELLSEPESLYSYLYQLQSD                                        
     Match   ********************

  Please check your alignment file header to be sure you correctly specified
  the starting and ending residue numbers and chains. The alignment sequence
  must match that from the atom file exactly.

  Another possibility is that some residues in the atom file are missing,
  perhaps because they could not be resolved experimentally. (Note that Modeller
  reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.)
  In this case, simply replace the section of your alignment corresponding
  to these missing residues with gaps.
read_te_288W> Protein not accepted:        2  1XEFA
rdabrk__337E> Structure not read in (please consult the log file
              for more details):



Please help.

Thanks and Regards

Ajeeta kaushiki
JNU