\relax \@writefile{toc}{\contentsline {section}{\numberline {1}Introduction and Methodology}{1}} \@writefile{toc}{\contentsline {section}{\numberline {2}Starting the program}{2}} \@writefile{toc}{\contentsline {section}{\numberline {3}Reading Structures}{3}} \newlabel{sec:read}{{3}{3}} \@writefile{toc}{\contentsline {section}{\numberline {4}Getting Help}{3}} \@writefile{toc}{\contentsline {section}{\numberline {5}Fitting Structures}{4}} \@writefile{toc}{\contentsline {section}{\numberline {6}Specifying Atom Subsets}{4}} \newlabel{sec:atoms}{{6}{4}} \@writefile{toc}{\contentsline {section}{\numberline {7}Specifying Zones}{5}} \newlabel{sec:zone}{{7}{5}} \@writefile{toc}{\contentsline {subsection}{\numberline {7.1}Sequence Alignment}{7}} \@writefile{toc}{\contentsline {subsection}{\numberline {7.2}Reading an Alignment}{7}} \@writefile{toc}{\contentsline {subsection}{\numberline {7.3}Limiting Zones Read From an Alignment}{7}} \@writefile{toc}{\contentsline {subsection}{\numberline {7.4}Iterative Updating of the Fitting Zones}{8}} \newlabel{subsec:iterate}{{7.4}{8}} \@writefile{toc}{\contentsline {section}{\numberline {8}Multiple Structure Fitting}{8}} \newlabel{sec:multi}{{8}{8}} \@writefile{toc}{\contentsline {subsection}{\numberline {8.1}Specifying Zones With Multiple Structure Fitting}{9}} \@writefile{toc}{\contentsline {section}{\numberline {9}Calculating the RMSd Over Other Zones and Atoms}{9}} \@writefile{toc}{\contentsline {section}{\numberline {10}Obtaining Output}{9}} \@writefile{toc}{\contentsline {subsection}{\numberline {10.1}The Fitted Structure}{9}} \@writefile{toc}{\contentsline {subsection}{\numberline {10.2}Centering the Coordinates}{10}} \@writefile{toc}{\contentsline {subsection}{\numberline {10.3}Details of the Fitting}{10}} \@writefile{toc}{\contentsline {subsection}{\numberline {10.4}By-residue RMS Deviation}{10}} \@writefile{toc}{\contentsline {section}{\numberline {11}Modifying the Fit}{11}} \@writefile{toc}{\contentsline {section}{\numberline {12}Miscellaneous Commands}{11}} \@writefile{toc}{\contentsline {section}{\numberline {13}Command Summary}{11}} \@writefile{toc}{\contentsline {section}{\numberline {14}Copyright}{13}} \@writefile{toc}{\contentsline {section}{\numberline {15}How do I Reference \unhbox \voidb@x \hbox {\bfseries ProFit}?}{14}}