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
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
Ben,
I truly admire your patience in answering the same question, but wouldn't it be easier to put few lines in mod9v7 script saying that if "import site failed" message appears below it should not be considered an error? It would save lots of initial frustration to beginners and also some internet bandwidth.
Just my 2c.
At 11:42 AM 6/25/2009, you wrote: >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
========================================================================== | Mensur Dlakic, PhD | Tel: (406) 994-6576 | | Department of Microbiology | Fax: (406) 994-4926 | | Montana State University | | | 109 Lewis Hall, P.O. Box 173520 | http://myprofile.cos.com/mensur | | Bozeman, MT 59717-3520 | E-mail: mdlakic@montana.edu | ==========================================================================
Dear, I am beginner in modeling of protein and when I try to use the Modeller 9v7 or 9v6 the following message appears on the first line permission denied. What should you do?
Alessandra
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Alessandra marques wrote: > I am beginner in modeling of protein and when I try to use the Modeller > 9v7 or 9v6 the following message appears on the first line permission > denied. What should you do?
Sorry, but this is a bit too vague. What kind of system are you trying to run Modeller on? What install package are you using? How are you trying to run it? What is the exact error message?
Ben Webb, Modeller Caretaker
Mensur Dlakic wrote: > I truly admire your patience in answering the same question, but > wouldn't it be easier to put few lines in mod9v7 script saying that if > "import site failed" message appears below it should not be considered > an error? It would save lots of initial frustration to beginners and > also some internet bandwidth.
This would probably really irritate expert users, including ourselves, so I'm not going to do that. But I will add such a message somewhere in the examples - thanks for the suggestion.
Ben Webb, Modeller Caretaker
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Alessandra marques -
Cool Hunk -
Mensur Dlakic -
Modeller Caretaker