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)?
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