Xdet Results (*.Xdet) --------------------- The files contain the whole list of positions in the alignments descendently sorted by the main score of the method (CORR: correlation between the aminoacid similarities within the position and the functional similarities between the corresponding proteins). pos aa entrop CORR local_Z local_P-val global_Z global_P-val 16 K 16 -1 2.714 - -1 xx 0.6493 5.1414 0.000000e+00 6.1201 1.298701e-05 76 E 76 -1 2.101 - -1 xx 0.5755 4.2625 0.000000e+00 5.4237 3.896104e-05 10 G 10 -1 2.247 - -1 xx 0.5481 4.6347 1.000000e-03 5.1655 9.090909e-05 .... .. pos Position number in the alignment (numbering includes gaps). Take a look at the corresponding *.eq file to see tue equivalence with the PDB numbers of the structure used to map the residues. aa Aminoacid of the first sequence in the alignment. entrop Entropy of the position in the alignment (full cons. => entrop=0). CORR MAIN SCORE of the method (see above). local_Z Z-score of that correlation with respect to a background distribution containing all the scores obtained for that position in the 1000 random sequence-function assignments. local_P-val P-value for the same distribution. global_Z Same as for "local_Z" but with respect to a background distribution containing all the scores for all the position in all the 1000 randomizations global_P-val Same as for "local_P-val" but with respect to a background distribution containing all the scores for all the position in all the 1000 randomizations MCdet Results (*.MCdet) ----------------------- The files contain the whole list of positions in the alignments descendently sorted by the main score of the method (DIST: distance between the vector of that aminoacid/position and the function in the MCA space). pos_aa DIST global_P-val local_P-val 117K 0.75592895 0 0 119D 0.75592895 0 0 15G 1.0141851 5.6461731e-06 0 16K 1.1338934 8.1555834e-06 0 .... .. pos_aa Position (alignment numbering -same as Xdet-) and aminoacid (# for gaps). DIST MAIN SCORE of the method (see above). global_P-val Same as for Xdet above local_P-val Same as for Xdet above PDB numbering (*.eq) -------------------- These files contain the equivalences between the alignment numbering and the PDB numbering of the structures used to map the results. RasMol scripts (*.sc) --------------------- RasMol scripts for for representing the results in RasMol. By default, the set of predicted residues commented in the paper (top of the lists) are shown. For selecting/unselecting other residues, please take into account the equivalences between the numbering in the result files and the PDB numbering (see previous point). For using these script follow these steps: 0) Install RasMol (if it is not). RasMol is free software which runs on most OS: http://www.umass.edu/microbio/rasmol/getras.htm 1) Edit the script (file.sc) with a text editor and, in the "load pdb" line, change the path and name of your local PDB file. 2) Start RasMol with that script: "rasmol -script file.sc" Another alternative: 1) Edit the scripts (file.sc) and comment the "load pdb" line by adding a "#" at the beginning (or remove the line). 2) Open RasMol and load the PDB structure as usual. 3) Within RasMol's command line enter: "script file.sc"