Software

Useful programs for nmr data processing and analysis, and modeling of  biomolecules.

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NMRPipe/Draw - nmr data processing

SPARKY - nmr data analysis

        SPARKY manual

CYANA - structure determination

        mailing list archives

        Guntert presentation/practical(pdf)

        DYANA manual

XPLOR-NIH - structure determination

AMBER - molecular dynamics simulations

    amber 8 manual

    searchable mailing list archives

    how-to...

    an AMBER publication list (not guaranteed to be comprehensive)

MODELFREE/FAST MODELFREE - nmr relaxation data analysis

    modelfree manual

    fast-modelfree manual  (hint: if you are getting errors when attempting to run fast modelfree, make sure that there are no underscores in the names of your files, and make sure that your files contain no extra lines (delete any extra space before/after the actual data lines).

TENSOR2 - nmr relaxation data analysis

    theory 

    practice exercise

HYDRONMR - calculation of theoretical          solution and nmr relaxation properties of biomolecules

    hydronmr user guide 

REDCAT -  analysis of residual dipolar couplings.

PALES - analysis of residual dipolar couplings. 

MODULE - analysis of residual dipolar couplings

     module manual

MOLMOL - biomolecule visualization

        molmol user guide

PYMOL - biomolecule visualization/movies

        pymol user guide

VMD - biomolecule visualization/movies

        VMD user guide

CHIMERA - biomolecule visualization (fastest/easiest for making movies of AMBER trajectories)

        chimera user guide