Thanks for suggestions again!
regarding S-S bridges I've understood well the method of the manual S-S bond definition using
model.patch() method. On other hand I wounder to know how alternative
model.patch_ss_templates() method could be implemented taking S-S from the templates. For instance using modeller advanced tutorial I've obtained results of the multiple-sequence alignment with the inclusion of the aligned sequence + several temples sequences (this output alignment is produced reasonable model). Next I used
patch_disulfides.py example with this alignment to obtain stereochemical restraints.
# Create the disulfide bonds using equivalent disulfide bonds in templates:
mdl.patch_ss_templates(aln)
# Create the stereochemical restraints
sel = selection(mdl)
mdl.restraints.make(sel, restraint_type='stereo', spline_on_site=False)
Now how I could perform such restrains-guided modelling to build model with the S-S bridges?