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

[Charlotte Habegger-Polomat <>]

Thank you for the help!

I did find my template sequences in $(LIB)/CHAINS_all.seq and now the 
sequence information is correct.

-Charlotte Habegger-Polomat
P.S. I am forwarding to the Modeller discussion group in case this may 
be of help to someone else



...but not
Guido Leoni wrote:

> Hi
> The env directory is the directory where your seq.files and your 
> structures are located. If they are in $(LIB)/CHAINS_all.seq ok.
> The log file tells you that your the align codes and the codes in the 
> seq.files are not the same check it and make you sure that they are 
> coincident
> I hope that I have helped
>
> 2005/9/16, Charlotte Habegger-Polomat < 
> <">mailto:>>:
>
>     Hello!
>
>     I have redone the basic tutorial successfully with the example given,
>     and would now like to reproduce those same steps with my protein of
>     interest. In my working directory, I have the PDB files for the
>     structures I'm trying to align and the following compare.py file:
>
>     ------------------------------------------------
>     env = environ()
>     aln = alignment(env, file='$(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
>
>
>
>
>
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