I need to obtain loop conformation distributions in a tetramer structure. So I
used loopmodel() to redefine the 4 loops in each subunit. I found that the 4
loops in each tetramer is not symmetrical. I therefore applied
model_symmetry_define() in order to fix them the same during the optimisation.
If you want to do loop modeling with symmetry restraints, you would be
better off overriding the special_restraints function in the loopmodel
class, rather than trying to do the entire optimization by hand. See,
for example, http://salilab.org/archives/modeller_usage/2005/msg00298.html
Also, what does aln.append_model(lop, align_codes='model-nam'+'_ini',
atom_files='tmp-nam'+'_ini') mean?
It adds the sequence of the model 'lop' to the alignment 'aln'. That
sequence can then be refered to with the align code 'model-nam_ini', and
if the structure corresponding to the sequence is required, Modeller
will read it from the atom file 'tmp-nam_ini'.
The erro message by executing the above .py file is:
"_modeller.error: transfe_682E> Structural information is not available for all
sequences in the alignment. Aborting."
This means that Modeller was unable to read the structural information
(i.e. atom coordinates) from the atom file. This is probably because you
called it 'tmp-nam_ini'. You probably want to call it the same thing as
your original PDB file, as in the example.