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 modeller-care@salilab.org wrote:

From: Modeller Caretaker modeller-care@salilab.org Subject: Re: [modeller_usage] Modelling Query To: "Cool Hunk" fascinatingheart2000@yahoo.com Cc: modeller_usage@salilab.org Date: Thursday, June 25, 2009, 9:34 AM

Cool Hunk wrote: > I am a new Modeller user, i am having some problems running Modeller, > while i run the script using command "*mod9v7 model.py*" it doesnt run > completely and generates errors

What errors? We can only help if you tell us what the errors are.

> but when i run the script using command > *"Python model.py" *it runs completely and generate all the pdb files of > models but not the log file for it even though i have included the > function "*log.verbose()"* in the script, and the same is the case for > model evaluation script and energies calculation script.....

Python doesn't generate log files - the output comes out on standard output (i.e. your screen, if you didn't direct it somewhere else). To get something very similar to running mod9v7, use something like

python model.py > model.log

> my other question is about the model evaluation, that do i have to run > the evaluation script for each model individually and the compare the > final dope scores or the scripts takes all the models at once and give > me the final good model???

You can do it either way. You can evaluate a single model with the script at http://salilab.org/modeller/9v7/manual/node242.html Alternatively you can have automodel assess every model it builds automatically by setting assess_methods; an example is at http://salilab.org/modeller/9v7/manual/node20.html

Ben Webb, Modeller Caretaker