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Helpful Utilities<= o:p>

 

mutinf_ten_choose_ten.csh <pdbfile&= gt; <base dir for run directories with torsion angle .x= vg files>

 

This is a shell scrip= t that runs MutInf with pretty default settings, witho= ut the Wilcoxon filtering.

 

 

create_reslist.pl <pdbfile> < base dir for run directori= es with torsion angle .xvg files>

 

This is called by the= above shell script to automatically make the residue file that maps pdb residues to .xvg file= s with the torsions.

If you have nonstanda= rd residue names you may have to modify this to account for these. I get around this by modifying the pdbfile to have only standard residue names. This is also so they are recognized as being part of the “Protein” selection by GROMACS.

 

table_to_resent_diag.pl <file.txt>

 

This perl script pulls diagonal elements out of MutInf ma= trices along with residue names-numbers. These diagonal elements (when nonzero) ha= ve the residue self-entropies corrected to second order. Output is f= ile_resent.csv .

 

replace_res_bfac_mut.pl <pdbfile> <datafi= le>

 

w= here datafile has a first column with residue name-numbers (i.e. ALA24) and a se= cond column containing values to replace the bfactor= entry in the pdb file, such as file_resent.csv= above.