[modeller_usage] Repeating basic tutorial with my protein - stuck at malign3d step

[Charlotte Habegger-Polomat <>]

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