PROCHECK parameters

Listing options

The following options govern the output in the .out file which gives the residue-by-residue listing (see Appendix D).

The 6 options are:-

Listing options
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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)

Description:-

Print explanatory text - Allows you to include or suppress the printing of the explanatory text which gives details such as the tables of "ideal" values against which your structure has been compared, and the keys to the various codes used in the print-out.

Print only asterisks denoting deviations and not values - Answering Y to this option shows only the asterisks on the listing. No values are printed.

Print only highlighted residues - Allows you to only print those residues which have any asterisked parameters.

Min. deviation from ideal for parameter to be printed - Defines the minimum deviation required in a parameter before it is printed. The default value is 0.0, meaning that all parameters are printed. If the value is set to, say, 2.0, only those parameters that deviate by 2.0 or more standard deviations from their ideal value will be shown.

Number of lines per page - Defines the number of lines to be printed before a page is thrown. It tells the program when to start a new page and hence when to print a new set of column headings. Normally, the standard is 66 lines per page, but your printer may print more or less per page, so amend this figure accordingly.

List the bad contacts - Determines whether the bad contacts are to be listed at the end of the print-out or not.

PROCHECK parameters