Greetings,
I am using python2.5.1 and modeller version 9v3 on a Mac desktop (OSX 10.4.8).
I saw a similar post in the discussion board regarding the compare.py script of the tutorial where the function call generated an error message. However, the information therein didn't really help me.
I also referred to the user manual and found that in my version of modeller, malign_3d has been deprecated and that I should use salign. However, salign (in the context of the tutorial exercise) does not return an object that can be used to continue the tutorial.
I am running the compare.py script from a directory on my Desktop separate from the modeller installation directory (should I be running the script from within the modeller directory?)
For posterity, I have included my 'version' of the compare.py script and the error message from the python interpreter.
Thanks for your time and consideration in this matter.
Michael Mayhew
<<< compare.py >>>
from modeller import *
env = environ() aln = alignment(env, file='pdball.pir', align_codes=('1b8pA', '1bdmA', '1civA', '5mdhA', '7mdhA', '1smkA'))
aln. malign() aln.malign3d() aln.compare_structures() aln.id_table(matrix_file='family.mat') env.dendogram(matrix_file='family.mat', cluster_cut=-1.0)
<<< python traceback error message >>>
Multiple dynamic programming alignment (MALIGN): Residue-residue metric : $(LIB)/as1.sim.mat ALIGN_BLOCK : 1 Gap introduction penalty: -900.0000 Gap extension penalty : -50.0000 Length of alignment : 384 pdbnam_____E> Filename for PDB code not found: 1b8p Directories: Extensions : :.atm:.pdb:.ent:.crd (Also tried prepending 'pdb', and looking for .Z, .gz, .bz2)
Traceback (most recent call last): File "compare.py", line 8, in <module> aln.malign3d() File "/Library/modeller-9v3/modlib/modeller/alignment.py", line 295, in malign3d edit_file_ext) IOError: pdbnam_____E> Filename for PDB code not found: 1b8p Directories: Extensions : :.atm:.pdb:.ent:.crd (Also tried prepending 'pdb', and looking for .Z, .gz, .bz2)