Cool Hunk wrote: > 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*
That's not an error; see http://salilab.org/modeller/release.html#issues
> 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()
Sure - that will do some simple checks of the alignment. But they are very simple checks, so will only detect very obvious errors in the alignment.
> 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
It looks like it couldn't open the PDB file for some reason, because it tried open a directory rather than a file. Check to make sure you don't have a directory with the same name as your PDB file.
Ben Webb, Modeller Caretaker