Hi, I am grateful for your immediate and so important replies. Althouth I face serious problem. One month I am trying to start modeller. My scripts are named script_1.top/script_2.top... but it is impossible to start my diploma theses. I thought the probability my script is wrong and so I tried to run a script of the modeller's tutorial but the message I got is the following:
[root@localhost test1]# mod9v3 TvLDH.ali 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 File "TvLDH.ali", line 1 >P1;TvLDH ^ SyntaxError: invalid syntax
This message I always recieve but I don't understand what is wrong because the python is installed. On top of that I 've tried to run modeller from the python interpreter but the output message told me that mod9v3 is a script and not a command. Please help me. I don't know what to do. Thank you. With best regards, Maria.
> [root@localhost test1]# mod9v3 TvLDH.ali 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 > File "TvLDH.ali", line 1 > >P1;TvLDH > ^ > SyntaxError: invalid syntax
1) For the platform dependent library warning see documentation: http://salilab.org/modeller/release.html#issues 2) Seems you are using the wrong argument. The argument for mod9v3 should be a script file (usually ending ".py" or ".top") and rather not your alignment file (".ali"). 3) It is generally not a good idea running software as root unless it is really necessary (which is not the case for modeller)
============================================ Dr Ralf Schmid Lecturer in Bioinformatics Department of Biochemistry Henry Wellcome Building University of Leicester Lancaster Road Leicester LE1 9HN UK
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