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Re: [modeller_usage] Modelling Query

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

> 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
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage