Hello!
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 $(LIB)/CHAINS_all.seq referred to.
If I need to change that line:
aln = alignment(env, file='$(LIB)/CHAINS_all.seq',
Then what type of file should I use?
This is the error message I am getting:
-----------------------------------------------------
File "compare.py", line 3, in ?
align_codes=('1n75', '1n77'))
File "/usr/local/packages/modeller8v1/modlib/modeller/alignment.py",
line 19, in __init__
self.__int_append('alignment.append', io, libs, vars)
File "/usr/local/packages/modeller8v1/modlib/modeller/alignment.py",
line 68, in __int_append
libs=libs.modpt, **vars)
File "/usr/local/packages/modeller8v1/modlib/modeller/util/top.py",
line 33, in read_alignment
return _modeller.read_alignment(aln, io, libs, *args)
_modeller.error: read_al_373E> Protein specified in ALIGN_CODES(i) was
not found in the alignment file; ALIGN_CODES( 1) = 1n75
----------------------------------------------------
and my compare.log:
-------------------------------------------------
Kind, OS, HostName, Kernel, Processor: 4, Linux pelican 2.6.7-gentoo-r11
i686
Date and time of compilation : 06/20/2005 12:04:54
MODELLER executable type : i386-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2005/09/16 11:37:06.955
read_al_373E> Protein specified in ALIGN_CODES(i) was not found
in the alignment file; ALIGN_CODES( 1) = 1n75
---
-----------------------------------------------
Thank you for any suggestions as to how I can compare the structures!
-Charlotte