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.