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 ============================================