PROCHECK-COMP. PROCHECK v.3.4.3 - Parameter file (procheck_comp.prm) ------------------------------- Note: Listing options and colour definitions are given at the end of the file. Colour all plots? ----------------- Y <- Produce all plots in colour (Y/N)? Which plots to produce ---------------------- Y <- 1. Ramachandran plot (Y/N)? Y <- 2. Gly & Pro Ramachandran plots (Y/N)? Y <- 3. Chi1-Chi2 plots (Y/N)? N <- 4. Residue Phi torsion angle plots (Y/N)? N <- 5. Residue Psi torsion angle plots (Y/N)? Y <- 6. Residue Chi-1 plots (Y/N)? Y <- 7. Residue Chi-2 plots (Y/N)? Y <- 8. Residue Ramachandran plots (Y/N)? N <- 9. Residue chi1-chi2 plots (Y/N)? Y <- 10. Ensemble geometry (Y/N)? Y <- 11. Residue property comparisons Y <- 12. Model-by-model secondary structures (Y/N)? +-----------------+ | PLOT PARAMETERS | +-----------------+ 1. Ramachandran plot -------------------- N <- Separate page for each structure (Y/N)? Y <- Shade in the different regions (Y/N)? Y <- Print the letter-codes identifying the different regions (Y/N)? Y <- Draw line-borders around the regions (Y/N)? N <- Show only the core region (Y/N)? 1 <- Label residues in: 0=disallow,1=generous,2=allow,3=core regions 1.0 <- Size of data-points (0.0-2.0) N <- Plot filled-in data points (Y/N)? Y <- Show model numbers inside data points (Y/N)? N <- Produce a COLOUR PostScript file (Y/N)? WHITE <- Background colour WHITE <- Region 0: Disallowed CREAM <- Region 1: Generous YELLOW <- Region 2: Allowed RED <- Region 3: Most favourable, core, region BLACK <- Colour of markers in favourable regions RED <- Colour of markers in unfavourable regions N <- Produce "publication version" of Ramachandran plot (Y/N)? 2. Gly & Pro Ramachandran plots ------------------------------- -3.0 <- Cut-off value for labelling of residues Y <- Plot all 20 Ramachandran plots (Y/N)? N <- Produce a COLOUR PostScript file (Y/N)? WHITE <- Background colour CREAM <- Lightest shaded regions on plots GREEN <- Darkest shaded regions on plots YELLOW <- Colour of markers in favourable regions RED <- Colour of markers in unfavourable regions 3. Chi1-Chi2 plots ------------------ -3.0 <- Cut-off value for labelling of residues N <- Produce a COLOUR PostScript file (Y/N)? WHITE <- Background colour CREAM <- Lightest shaded regions on plots GREEN <- Darkest shaded regions on plots YELLOW <- Colour of markers in favourable regions RED <- Colour of markers in unfavourable regions 4-9. Dihedral angle frequency distributions ------------------------------------------- N <- Plot histograms, rather than show successive values (Y/N)? 0.0 <- Circ. var. cut-off (residues with lower values not plotted) Y <- Background shading (Y/N)? N <- Produce a COLOUR PostScript file (Y/N)? WHITE <- Background colour of page CREAM <- Background colour on graphs PURPLE <- Shading of region representing dihedral angle restraints YELLOW <- Colour for favourable G-factor scores RED <- Colour for unfavourable G-factor scores YELLOW <- Colour for accessibility & circular variance dials N <- Omit circular variance value and dial (Y/N)? N <- Omit G-factor value and shaded square (Y/N)? N <- Omit accessibility symbol (Y/N)? N <- Splay model-numbering on the 2D plots (Y/N)? 10. Ensemble geometry --------------------- 1 2 < Which 2 main graphs to be printed (see Note 2 for full list) Y <- Background shading on main graphs (Y/N)? 2.0 <- Number of standard deviations for highlighting Y <- Show shading representing estimated accessibility (Y/N)? N <- Produce a COLOUR PostScript file (Y/N)? WHITE <- Background colour CREAM <- Background shading on main graphs PURPLE <- Colour of histogram bars on main graphs RED <- Colour of highlighted histogram bars BLUE <- Minimum accessibility colour (buried regions) WHITE <- Maximum accessibility colour YELLOW <- Colour for favourable G-factor scores RED <- Colour for unfavourable G-factor scores YELLOW <- Colour for schematic of the secondary structure YELLOW <- Colour for accessibility & circular variance dials Note 2 ------ The 2 main graphs on the Ensemble Residue properties plot can be any 2 from the following list of options:- 1. Absolute deviation from mean Chi-1 value (excl. Pro) 2. Absolute deviation from mean of omega torsion 3. C-alpha chirality: abs. deviation of zeta torsion 11. Residue property comparisons -------------------------------- Y <- Background shading (Y/N)? N <- Produce a COLOUR PostScript file (Y/N)? WHITE <- Background colour CREAM <- Background shading on each graph PURPLE <- Colour of band 12. Model-by-model secondary structures --------------------------------------- Y <- Show shading representing estimated accessibility (Y/N)? N <- Produce a COLOUR PostScript file (Y/N)? WHITE <- Background colour BLUE <- Minimum accessibility colour (buried regions) WHITE <- Maximum accessibility colour YELLOW <- Colour for schematic of the secondary structure Colours (up to 50 can be defined) ------- 0.0000 0.0000 0.0000 'BLACK' <- Colour 1 1.0000 1.0000 1.0000 'WHITE' <- Colour 2 1.0000 0.0000 0.0000 'RED' <- Colour 3 0.0000 1.0000 0.0000 'GREEN' <- Colour 4 0.0000 0.0000 1.0000 'BLUE' <- Colour 5 1.0000 1.0000 0.0000 'YELLOW' <- Colour 6 1.0000 0.7000 0.0000 'ORANGE' <- Colour 7 0.5000 1.0000 0.0000 'LIME GREEN' <- Colour 8 0.5000 0.0000 1.0000 'PURPLE' <- Colour 9 0.5000 1.0000 1.0000 'CYAN' <- Colour 10 1.0000 0.5000 1.0000 'PINK' <- Colour 11 0.3000 0.8000 1.0000 'SKY BLUE' <- Colour 12 1.0000 1.0000 0.7000 'CREAM' <- Colour 13 0.0000 1.0000 1.0000 'TURQUOISE' <- Colour 14 1.0000 0.0000 1.0000 'LILAC' <- Colour 15 0.8000 0.0000 0.0000 'BRICK RED' <- Colour 16 0.5000 0.0000 0.0000 'BROWN' <- Colour 17 0.9700 0.9700 0.9700 'LIGHT GREY' <- Colour 18 0.9000 0.9000 0.9000 'MID GREY' <- Colour 19 0.8000 0.0000 1.0000 'MAUVE' <- Colour 20 -------------------------------------------------------------------------- File-handles ------------ N <- Add 9-character description of plot to each plot filename (Y/N)? (eg p1gcr_01_ramachand.ps, rather than p1gcr_01.ps) Y <- Print name of plotfile in bottom-left corner of plot (Y/N)? Y <- Combine all pages of same plot into single PostScript file (Y/N)? --------------------------------------------------------------------------