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