1.1 --- a/allpy/structure.py	Thu Mar 15 23:17:23 2012 +0400
     1.2 +++ b/allpy/structure.py	Fri Mar 16 00:10:42 2012 +0400
     1.3 @@ -511,8 +511,11 @@
     1.4          Other sequences are fitted to the main sequence, using all the columns
     1.5          from any block, which contains both sequences.
     1.6  
     1.7 +        All involved chains are shown with sticks, transparency=0.6
     1.8 +        (only backbone C, N and CA atoms).
     1.9 +        Atoms, involved in blocks, are shown with cartoon.
    1.10 +
    1.11          TODO: Each block is shown in one pymol frame.
    1.12 -        NOTE: Hide everything except involved chains, represented as cartoon
    1.13          """
    1.14          def sequence_to_pdb(s):
    1.15              return pdb_id_parse(s.pdb_chain.get_parent().get_parent().get_id())['code']
    1.16 @@ -550,7 +553,13 @@
    1.17                   'fit_from': columns_line(columns, fit_from) + " and name ca"})
    1.18          file.write("hide everything, all\n")
    1.19          for s in self.sequences:
    1.20 -            file.write("show cartoon, %(seq)s\n" % {'seq': sequence_line(s)})
    1.21 +            file.write("show sticks, %(seq)s and name c+n+ca\n" %
    1.22 +                {'seq': sequence_line(s)})
    1.23 +        for block in blocks:
    1.24 +            for s in block.sequences:
    1.25 +                file.write("show cartoon, %(seq)s\n" %
    1.26 +                    {'seq': columns_line(block.columns, s)})
    1.27 +        file.write("set stick_transparency, 0.6, all\n")
    1.28  
    1.29  class BlockMixin(base.Block, AlignmentMixin):
    1.30      """Mixin to add 3D properties to blocks.