Hi,
> [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)
Cheers,
Ralf
============================================
Dr Ralf Schmid
Lecturer in Bioinformatics
Department of Biochemistry
Henry Wellcome Building
University of Leicester
Lancaster Road
Leicester LE1 9HN UK
Tel. +44 (0)116 229 7023
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