Hi:
I would like to build a model staring from my own model. but it didn't work, it is said:
-------log--------------
_modeller.ModellerError: 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 " ", chain " "; atom file name: init.pdb
--------------------------
In fact in the alignment file I already add something like this:
-------------------align----------------------------
>P1;seq
sequence:seq: : : : ::: 0.00: 0.00
aaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
>P1;init
structureX:init.pdb:1 :A: :A:::-1.00:-1.00
aaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
>P1;temp
structureX:temp.pdb:1 :A: :A:::-1.00:-1.00
aaaaaaaaaaaaaaaaaabbbbbbbbbbbb
----------script-------------------------------------
class MyModel(automodel):
def special_restraints(self, aln):
rsr = self.restraints
at = self.atoms
# Two beta-strands:
rsr.add(secondary_structure.strand(self.residue_range('146:', '150:')))
rsr.add(secondary_structure.strand(self.residue_range('156:', '161:')))
a = MyModel(env,
alnfile='mult.ali',
knowns=('tempA'),
sequence='my',
inifile = 'init.pdb')
a.starting_model = 1
a.ending_model = 2
----------------------------------------------------------------------------
the seq and init share the same sequences. The starting model init.pdb contains a china named A.
could you give me some advices?
THX