Charlotte Habegger-Polomat wrote:
I have redone the basic tutorial successfully with the example given,
and would now like to reproduce those same steps with my protein of
interest. In my working directory, I have the PDB files for the
structures I'm trying to align and the following compare.py file:
------------------------------------------------
env = environ()
aln = alignment(env, file='$(LIB)/CHAINS_all.seq',
align_codes=('1n75', '1n77'))
aln.malign()
aln.malign3d()
aln.compare_structures()
aln.id_table()
env.dendrogram()
---------------------------------------------------
I was not sure what $(LIB)/CHAINS_all.seq referred to.
$(LIB) refers to the directory containing Modeller library files (usually the modlib/ subdirectory wherever you installed Modeller). CHAINS_all.seq is simply a file in PIR alignment format which contains the sequence of every chain in the PDB (as of the last Modeller update).
In your case, you can either use this file directly, since 1n75 and 1n77 are both in there (although you will also need to specify the chain identifier, so it'll be 1n75A and either 1n77A or 1n77B) or you can read the sequences from the PDB files themselves using the alignment.append_model() command:
http://salilab.org/modeller/manual/node181.html
Ben Webb, Modeller Caretaker
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