OOPS2 Model Analysis
Relevant web sites:
Summary
OOPS2 (developed by Gerard J. Kleywegt; see above link) is a program that
facilitates model rebuilding in "O" during structure refinement.
It takes structure analysis output from other programs (typically "O" and
"WhatCheck"), generates some of its own structure analysis, then incorporates
this information into an automatically generated mega-macro for "O" that
enables one to sequentially examine bad regions of the model, as defined
by the structure analysis data (e.g., phi-psi outliers, poor agreement
of sidechain conformation with most common rotamers, poor model fit to
electron density). Using OOPS2 involves the following steps:
i) generate necessary output datablocks from "O", ii) run OOPS2, indicating
the analyses of interest and the corresponding "O" datablocks, which generates
a mega-macro (oops.omac), and iii) invoke the macro from within "O" (@oops.omac).
The macro causes the "O" user menu to be automatically updated with additional
options that allows for sequentially advancing to "bad" residues.
Advancing to each residue is accompanied by text output at the command
prompt that describes the "bad" feature. Additionally added to the
user menu by the oops macro are selectable options that allow output of
a table that assigns a number to each residue according to the perceived
problem at each "bad" residue (0=good fit to good density, 1=poor fit to
good density, 2=poor density, 3=no density).
Generation of output files from O