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