PROCHECK-NMR. PROCHECK v.3.4 - Parameter file (procheck_nmr.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
----------------------
a. Geometry plots
--------------
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. Equivalent resolution (Y/N)?
Y <- 12. Model-by-model secondary structures (Y/N)?
b. Restraint analyses
------------------
Y <- 13. Distance restraints plot (Y/N)?
Y <- 14. Restraint differences plot (Y/N)?
Y <- 15. Numbers of distance restraints (Y/N)?
Y <- 16. Actual distance - restraint summary (Y/N)?
Y <- 17. Violation frequency summary (Y/N)?
Y <- 18. Restraint statistics (Y/N)?
N <- 19. Restraint spans (Y/N)?
Y <- 20. Residue-by-residue restraint violations (Y/N)?
Y <- 21. Model-by-model violations (Y/N)?
+-----------------+
| PLOT PARAMETERS |
+-----------------+
a. G E O M E T R Y P L O T S
1. Ramachandran plot
--------------------
N <- Separate page for each model in the ensemble (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
-------------------------------------------
Y <- 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. Equivalent resolution
-------------------------
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
b. R E S T R A I N T A N A L Y S E S
General parameters
------------------
N <- Define short/medium/long-range restraints by dist - see Note (Y/N)?
0.0 3.5 <- Upper and lower distance defining short-range restraints
3.5 5.0 <- " " " " " medium-range "
5.0 10.0 <- " " " " " long-range "
YELLOW <- Colour for long-range restraints
LIME GREEN <- Colour for medium-range restraints
CYAN <- Colour for short-range restraints
Note
----
If the above parameter is set to Y, the restraints will be classed as
short, medium or long-range according to the distance ranges defined above.
If the parameter is set to N, the default definition will be taken where
the ranges depend on the sequence separation of the residues involved in
each restraint, as follows:-
Short-range - restraint is between atoms of same residue
Medium-range - restraint links residues whose sequence separation
is between i + 1 and i + 4
Long-range - restraint links residues whose sequence separation
is greater than 4 residues
13-14. Distance restraints and Restrain differences plots
---------------------------------------------------------
Y <- Include all short-range restraints (as defined above) (Y/N)?
Y <- " " medium-range " " " " (Y/N)?
Y <- " " long-range " " " " (Y/N)?
Y <- Include NOE distance restraints (Y/N)?
Y <- Include H-bond distance restraints (Y/N)?
Y <- Include disulphide distance restraints (Y/N)?
Y <- Show only violated restraints (Y/N)?
Y <- Exclude duplicate restraints within the same residue (Y/N)?
Y <- Background shading on main graphs (Y/N)?
N <- Produce a COLOUR PostScript file (Y/N)?
WHITE <- Background colour
CREAM <- Background shading on main graphs
PINK <- Shading for regions outside upper restraint bounds
ORANGE <- Shading for regions outside lower restraint bounds
15-17. Summaries of distance restraints and differences
-------------------------------------------------------
Y <- Separate page for each graph (Y/N)?
Y <- Background shading on main graphs (Y/N)?
N <- Produce a COLOUR PostScript file (Y/N)?
WHITE <- Background colour
CREAM <- Background shading on main graphs
PURPLE <- Colour for upper-bound restraints
SKY BLUE <- Colour for lower-bound restraints
RED <- Colour for upper-bound restraint violations
PINK <- Colour for lower-bound restraint violations
18. Restraint statistics
------------------------
N <- Produce a COLOUR PostScript file (Y/N)?
WHITE <- Background colour
PURPLE <- Colour for upper-bound restraints
SKY BLUE <- Colour for lower-bound restraints
RED <- Colour for upper-bound restraint violations
PINK <- Colour for lower-bound restraint violations
19-21. Restraint spans, residue-by-residue and model-by-model violations
------------------------------------------------------------------------
Y <- Include all short-range restraints (as defined above) (Y/N)?
Y <- " " medium-range " " " " (Y/N)?
Y <- " " long-range " " " " (Y/N)?
Y <- Include NOE distance restraints (Y/N)?
Y <- Include H-bond distance restraints (Y/N)?
Y <- Include disulphide distance restraints (Y/N)?
Y <- Background shading on main graphs (Y/N)?
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
BLUE <- Minimum accessibility colour (buried regions)
WHITE <- Maximum accessibility colour
SKY BLUE <- 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 dials
CYAN <- Colour for histograms of restraints per residue
RED <- Colour for restraint violations
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
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File-handles
------------
N <- Add 9-character description of plot to each plot filename (Y/N)?
(eg p1nmr_01_ramachand.ps, rather than p1nmr_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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