PROCHECK v.3.3 - Parameter file (procheck.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)? Y <- 4. Main-chain parameters (Y/N)? Y <- 5. Side-chain parameters (Y/N)? Y <- 6. Residue properties (Y/N)? Y <- 7. Main-chain bond length distributions (Y/N)? Y <- 8. Main-chain bond angle distributions (Y/N)? Y <- 9. RMS distances from planarity (Y/N)? Y <- 10. Distorted geometry plots (Y/N)? +-----------------+ | PLOT PARAMETERS | +-----------------+ 1. Ramachandran plot -------------------- 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 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. Main-chain parameters ------------------------ 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 5. Side-chain parameters ------------------------ 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 6. Residue properties --------------------- 1 2 3 < Which 3 main graphs to be printed (see Note 1 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 RED <- Region 0: Disallowed PINK <- Region 1: Generous GREEN <- Region 2: Allowed SKY BLUE <- Region 3: Most favourable, core, region YELLOW <- Colour for favourable G-factor scores RED <- Colour for unfavourable G-factor scores YELLOW <- Colour for schematic of the secondary structure Note 1 ------ The 3 main graphs on the Residue properties plot can be any 3 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 4. Absolute deviation from mean of H-bond energy 5. Gamma atom B-value 6. Average B-value of main-chain atoms 7. Average B-value of side-chain atoms 8. G-factor for phi-psi distribution 9. G-factor for chi1-chi2 distribution 10. Residue-by-residue G-factor 11. Approx. accessibility (estimated by Ooi numbers) 12. Percentage residue main-chain accessibility 13. Standard deviation of main-chain B-values 14. Standard deviation of side-chain B-values 7. Main-chain bond length distributions --------------------------------------- Y <- Background shading on graphs (Y/N)? 2.0 <- Number of standard deviations for highlighting N <- Produce a COLOUR PostScript file (Y/N)? WHITE <- Background colour of page CREAM <- Background shading on graphs PURPLE <- Colour of histogram bars RED <- Colour of highlighted histogram bars 8. Main-chain bond angle distributions -------------------------------------- Y <- Background shading on graphs (Y/N)? 2.0 <- Number of standard deviations for highlighting N <- Produce a COLOUR PostScript file (Y/N)? WHITE <- Background colour of page CREAM <- Background shading on graphs PURPLE <- Colour of histogram bars RED <- Colour of highlighted histogram bars 9. RMS distances from planarity ------------------------------- Y <- Background shading on graphs (Y/N)? 0.03 <- RMS distance for highlighting for ring groups 0.02 <- " " " " " other groups N <- Produce a COLOUR PostScript file (Y/N)? WHITE <- Background colour of page CREAM <- Background shading on graphs PURPLE <- Colour of histogram bars RED <- Colour of highlighted histogram bars 10. Distorted geometry plots ---------------------------- 0.05 <- Deviation from "ideal" bond-length (A) 10.0 <- Deviation from "ideal" bond-angle (degrees) 0.03 <- RMS distance from plane for ring atoms 0.02 <- " " " " for other atoms N <- Produce a COLOUR PostScript file (Y/N)? CREAM <- Background colour of page BLUE <- Colour of "ideal" bond-lengths and angles RED <- Colour of actual bond-lengths/angles/planes GREEN <- Colour for lettering showing differences from ideals Listing options --------------- Y <- Print explanatory text at head of parameters listing (Y/N) N <- Print only asterisks denoting deviations, and not the values (Y/N) N <- Print only highlighted residues (Y/N) 0.0 <- Min. deviation from ideal required for parameter to be printed 66 <- Number of lines per page on parameters listing Y <- List the bad contacts (Y/N) Colours ------- 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 0.8000 0.5000 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 1.0000 1.0000 1.0000 'WHITE' <- Colour 19 1.0000 1.0000 1.0000 'WHITE' <- Colour 20 G-factors --------- Y <- Use Engh & Huber means for bond length/angle G-factors(Y/N)? 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)? --------------------------------------------------------------------------