Hi, While I was running the second script which is called compare.py and is the following:
from modeller import *
env = environ() aln = alignment(env) for (pdb, chain) in (('1b8p', 'A'), ('1bdm', 'A'), ('1civ', 'A'), ('5mdh', 'A'), ('7mdh', 'A'), ('1smk', 'A')): m = model(env, file=pdb, model_segment=('FIRST:'+chain, 'LAST:'+chain)) aln.append_model(m, atom_files=pdb, align_codes=pdb+chain) aln.malign() aln.malign3d() aln.compare_structures() aln.id_table(matrix_file='family.mat') env.dendrogram(matrix_file='family.mat', cluster_cut=-1.0)
I recieved the following message and I don't know what to do.
suse:/home/maria # mod9v3 compare.py Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] 'import site' failed; use -v for traceback Traceback (most recent call last): File "compare.py", line 7, in ? m = model(env, file=pdb, model_segment=('FIRST:'+chain, 'LAST:'+chain)) File "/usr/lib/modeller9v3/modlib/modeller/model.py", line 23, in __init__ self.read(**vars) File "/usr/lib/modeller9v3/modlib/modeller/model.py", line 68, in read model_format, model_segment) 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, .bz. .bz2)
Please, help me.