Dear Ben,
Thank you so much for the instant response, i have understood what you have told, but following is the error messege i get when i use the command "mod9v7 model.py"
mod9v7 evaluate_model.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 my second question is about checking the reliability of an alignment in PIR format which we use to generate models... as i have generate this alignment after doing hand threading so i want to check its reliabilty, please tell me if i can do it using following script:
# Example for: alignment.append(), alignment.write(),
# alignment.check() # Read an alignment, write it out in the 'PAP' format, and
# check the alignment of the N-1 structures as well as the # alignment of the N-th sequence with each of the N-1 structures. from modeller import *
log.level(output=1, notes=1, warnings=1, errors=1, memory=0)
env = environ() env.io.atom_files_directory = '../atom_files' aln = alignment(env)
aln.append(file='ompA-1mal-align.ali ', align_codes='all') aln.write(file='ompA-1mal.pap', alignment_format='PAP') aln.write(file='ompA-1mal.fasta', alignment_format='FASTA') aln.check() as i have run this script i got following error, first using the "mod9v7 align.py" the same error messege i got for "mod9v7 model.py" and the remaining error messeges are about the alignment format which i could not understand
mod9v7 align.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 "align.py", line 18, in ? aln.check() File "/usr/lib/modeller9v7/modlib/modeller/alignment.py", line 198, in check self.check_structure_structure(io=io) File "/usr/lib/modeller9v7/modlib/modeller/alignment.py", line 207, in check_structure_structure return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst) IOError: readlinef__E> Error encountered on file read: Is a directory thanking in advance
Muhammad Noon
--- On Thu, 6/25/09, Modeller Caretaker <> wrote:
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