\documentclass[10pt,a4paper]{article}

% Packages
\usepackage{fancyhdr}           % For header and footer
\usepackage{multicol}           % Allows multicols in tables
\usepackage{tabularx}           % Intelligent column widths
\usepackage{tabulary}           % Used in header and footer
\usepackage{hhline}             % Border under tables
\usepackage{graphicx}           % For images
\usepackage{xcolor}             % For hex colours
%\usepackage[utf8x]{inputenc}    % For unicode character support
\usepackage[T1]{fontenc}        % Without this we get weird character replacements
\usepackage{colortbl}           % For coloured tables
\usepackage{setspace}           % For line height
\usepackage{lastpage}           % Needed for total page number
\usepackage{seqsplit}           % Splits long words.
%\usepackage{opensans}          % Can't make this work so far. Shame. Would be lovely.
\usepackage[normalem]{ulem}     % For underlining links
% Most of the following are not required for the majority
% of cheat sheets but are needed for some symbol support.
\usepackage{amsmath}            % Symbols
\usepackage{MnSymbol}           % Symbols
\usepackage{wasysym}            % Symbols
%\usepackage[english,german,french,spanish,italian]{babel}              % Languages

% Document Info
\author{leilaP}
\pdfinfo{
  /Title (pymol-basic.pdf)
  /Creator (Cheatography)
  /Author (leilaP)
  /Subject (Pymol\_Basic Cheat Sheet)
}

% Lengths and widths
\addtolength{\textwidth}{6cm}
\addtolength{\textheight}{-1cm}
\addtolength{\hoffset}{-3cm}
\addtolength{\voffset}{-2cm}
\setlength{\tabcolsep}{0.2cm} % Space between columns
\setlength{\headsep}{-12pt} % Reduce space between header and content
\setlength{\headheight}{85pt} % If less, LaTeX automatically increases it
\renewcommand{\footrulewidth}{0pt} % Remove footer line
\renewcommand{\headrulewidth}{0pt} % Remove header line
\renewcommand{\seqinsert}{\ifmmode\allowbreak\else\-\fi} % Hyphens in seqsplit
% This two commands together give roughly
% the right line height in the tables
\renewcommand{\arraystretch}{1.3}
\onehalfspacing

% Commands
\newcommand{\SetRowColor}[1]{\noalign{\gdef\RowColorName{#1}}\rowcolor{\RowColorName}} % Shortcut for row colour
\newcommand{\mymulticolumn}[3]{\multicolumn{#1}{>{\columncolor{\RowColorName}}#2}{#3}} % For coloured multi-cols
\newcolumntype{x}[1]{>{\raggedright}p{#1}} % New column types for ragged-right paragraph columns
\newcommand{\tn}{\tabularnewline} % Required as custom column type in use

% Font and Colours
\definecolor{HeadBackground}{HTML}{333333}
\definecolor{FootBackground}{HTML}{666666}
\definecolor{TextColor}{HTML}{333333}
\definecolor{DarkBackground}{HTML}{A3A3A3}
\definecolor{LightBackground}{HTML}{F3F3F3}
\renewcommand{\familydefault}{\sfdefault}
\color{TextColor}

% Header and Footer
\pagestyle{fancy}
\fancyhead{} % Set header to blank
\fancyfoot{} % Set footer to blank
\fancyhead[L]{
\noindent
\begin{multicols}{3}
\begin{tabulary}{5.8cm}{C}
    \SetRowColor{DarkBackground}
    \vspace{-7pt}
    {\parbox{\dimexpr\textwidth-2\fboxsep\relax}{\noindent
        \hspace*{-6pt}\includegraphics[width=5.8cm]{/web/www.cheatography.com/public/images/cheatography_logo.pdf}}
    }
\end{tabulary}
\columnbreak
\begin{tabulary}{11cm}{L}
    \vspace{-2pt}\large{\bf{\textcolor{DarkBackground}{\textrm{Pymol\_Basic Cheat Sheet}}}} \\
    \normalsize{by \textcolor{DarkBackground}{leilaP} via \textcolor{DarkBackground}{\uline{cheatography.com/36664/cs/11524/}}}
\end{tabulary}
\end{multicols}}

\fancyfoot[L]{ \footnotesize
\noindent
\begin{multicols}{3}
\begin{tabulary}{5.8cm}{LL}
  \SetRowColor{FootBackground}
  \mymulticolumn{2}{p{5.377cm}}{\bf\textcolor{white}{Cheatographer}}  \\
  \vspace{-2pt}leilaP \\
  \uline{cheatography.com/leilap} \\
  \end{tabulary}
\vfill
\columnbreak
\begin{tabulary}{5.8cm}{L}
  \SetRowColor{FootBackground}
  \mymulticolumn{1}{p{5.377cm}}{\bf\textcolor{white}{Cheat Sheet}}  \\
   \vspace{-2pt}Not Yet Published.\\
   Updated 20th April, 2017.\\
   Page {\thepage} of \pageref{LastPage}.
\end{tabulary}
\vfill
\columnbreak
\begin{tabulary}{5.8cm}{L}
  \SetRowColor{FootBackground}
  \mymulticolumn{1}{p{5.377cm}}{\bf\textcolor{white}{Sponsor}}  \\
  \SetRowColor{white}
  \vspace{-5pt}
  %\includegraphics[width=48px,height=48px]{dave.jpeg}
  Measure your website readability!\\
  www.readability-score.com
\end{tabulary}
\end{multicols}}




\begin{document}
\raggedright
\raggedcolumns

% Set font size to small. Switch to any value
% from this page to resize cheat sheet text:
% www.emerson.emory.edu/services/latex/latex_169.html
\footnotesize % Small font.

\begin{multicols*}{2}

\begin{tabularx}{8.4cm}{x{5.12 cm} x{2.88 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{2}{x{8.4cm}}{\bf\textcolor{white}{Set up}}  \tn
% Row 0
\SetRowColor{LightBackground}
Set working directory & `cd C:\textbackslash{}Users\textbackslash{}...` \tn 
% Row Count 2 (+ 2)
% Row 1
\SetRowColor{white}
Load pdb file from pdb website & `fetch 1ubq` \tn 
% Row Count 4 (+ 2)
% Row 2
\SetRowColor{LightBackground}
Load pdb file from local disk & `load 1ubq.pdb` \tn 
% Row Count 6 (+ 2)
\hhline{>{\arrayrulecolor{DarkBackground}}--}
\end{tabularx}
\par\addvspace{1.3em}

\begin{tabularx}{8.4cm}{x{4.16 cm} x{3.84 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{2}{x{8.4cm}}{\bf\textcolor{white}{Log files}}  \tn
% Row 0
\SetRowColor{LightBackground}
new log file & `log\_open file\_name.pml` \tn 
% Row Count 2 (+ 2)
% Row 1
\SetRowColor{white}
save and quit log file & `log\_close` \tn 
% Row Count 4 (+ 2)
% Row 2
\SetRowColor{LightBackground}
comment & \# \tn 
% Row Count 5 (+ 1)
% Row 3
\SetRowColor{white}
record the view coordinate & `get\_view` \tn 
% Row Count 7 (+ 2)
% Row 4
\SetRowColor{LightBackground}
run a log as a script & `@file\_name.pml \tn 
% Row Count 9 (+ 2)
\hhline{>{\arrayrulecolor{DarkBackground}}--}
\SetRowColor{LightBackground}
\mymulticolumn{2}{x{8.4cm}}{resume log file = run then edit at the end \newline append log file = edit at the end without running}  \tn 
\hhline{>{\arrayrulecolor{DarkBackground}}--}
\end{tabularx}
\par\addvspace{1.3em}

\begin{tabularx}{8.4cm}{x{4.56 cm} x{3.44 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{2}{x{8.4cm}}{\bf\textcolor{white}{Selection}}  \tn
% Row 0
\SetRowColor{LightBackground}
select selection\_name, selection\_expression & `select carbon\_beta, n. cb` \tn 
% Row Count 3 (+ 3)
% Row 1
\SetRowColor{white}
select selection\_name= (selection expression) & `select carbon\_beta = (n; cb)` \tn 
% Row Count 6 (+ 3)
\hhline{>{\arrayrulecolor{DarkBackground}}--}
\SetRowColor{LightBackground}
\mymulticolumn{2}{x{8.4cm}}{logical operator: and (/), not, or. !order of precedence -{}-\textgreater{} use ()}  \tn 
\hhline{>{\arrayrulecolor{DarkBackground}}--}
\end{tabularx}
\par\addvspace{1.3em}

\begin{tabularx}{8.4cm}{x{5.472 cm} p{0.988 cm} p{1.14 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{3}{x{8.4cm}}{\bf\textcolor{white}{Selection - single word}}  \tn
% Row 0
\SetRowColor{LightBackground}
All atoms & all & * \tn 
% Row Count 1 (+ 1)
% Row 1
\SetRowColor{white}
No atoms & none & none \tn 
% Row Count 2 (+ 1)
% Row 2
\SetRowColor{LightBackground}
All hydrogen atoms & hydro & h. \tn 
% Row Count 3 (+ 1)
% Row 3
\SetRowColor{white}
All atoms from HETATM record & het & \seqsplit{hetatm} \tn 
% Row Count 4 (+ 1)
\hhline{>{\arrayrulecolor{DarkBackground}}---}
\end{tabularx}
\par\addvspace{1.3em}

\begin{tabularx}{8.4cm}{x{5.852 cm} p{0.988 cm} p{0.76 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{3}{x{8.4cm}}{\bf\textcolor{white}{Porperty selector identifiers}}  \tn
% Row 0
\SetRowColor{LightBackground}
Atom by chemical symbol \{\{nl\}\} ex: Oxygen = O & \seqsplit{symbol} & e. \tn 
% Row Count 2 (+ 2)
% Row 1
\SetRowColor{white}
Atom/nucleic acid by code \{\{nl\}\} ex: Cα = ca, Cβ = cb & name & n \tn 
% Row Count 4 (+ 2)
% Row 2
\SetRowColor{LightBackground}
Aa/nucleic acid by code \{\{nl\}\}ex: Asparagine = asp / adenosine = a & resn & r \tn 
% Row Count 7 (+ 3)
% Row 3
\SetRowColor{white}
residue identifier (1-9999) & resi & i \tn 
% Row Count 8 (+ 1)
% Row 4
\SetRowColor{LightBackground}
PDB chain identifier (check in PDB file if letter or number ID) & chain & c \tn 
% Row Count 11 (+ 3)
% Row 5
\SetRowColor{white}
Secondary structure: \{\{nl\}\} α helix = 'H',  β strand = "S", Loop = 'L' & ss & ss \tn 
% Row Count 14 (+ 3)
\hhline{>{\arrayrulecolor{DarkBackground}}---}
\SetRowColor{LightBackground}
\mymulticolumn{3}{x{8.4cm}}{carbon α : first carbon bond to the side chain \newline carbon β : second carbon bond to the side chain}  \tn 
\hhline{>{\arrayrulecolor{DarkBackground}}---}
\end{tabularx}
\par\addvspace{1.3em}

\begin{tabularx}{8.4cm}{X}
\SetRowColor{DarkBackground}
\mymulticolumn{1}{x{8.4cm}}{\bf\textcolor{white}{selection macros}}  \tn
% Row 0
\SetRowColor{LightBackground}
\mymulticolumn{1}{x{8.4cm}}{\seqsplit{/object−name/segi−identifier/chain−identifier/resi−identifier/name−identifier}} \tn 
% Row Count 2 (+ 2)
% Row 1
\SetRowColor{white}
\mymulticolumn{1}{x{8.4cm}}{start by "/": start from the top of the hierarchie (object-name)} \tn 
% Row Count 4 (+ 2)
% Row 2
\SetRowColor{LightBackground}
\mymulticolumn{1}{x{8.4cm}}{end by "/": start from the bottom of the hierarchie (name-id)} \tn 
% Row Count 6 (+ 2)
% Row 3
\SetRowColor{white}
\mymulticolumn{1}{x{8.4cm}}{// :skip one level of hierarchie} \tn 
% Row Count 7 (+ 1)
% Row 4
\SetRowColor{LightBackground}
\mymulticolumn{1}{x{8.4cm}}{ex: `select lys, /helix\_alpha///lys` \{\{nl\}\} select all the residue of lysine from the object "helix\_alpha"} \tn 
% Row Count 10 (+ 3)
\hhline{>{\arrayrulecolor{DarkBackground}}-}
\end{tabularx}
\par\addvspace{1.3em}

\begin{tabularx}{8.4cm}{x{3.92 cm} x{4.08 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{2}{x{8.4cm}}{\bf\textcolor{white}{Diplay}}  \tn
% Row 0
\SetRowColor{LightBackground}
show the selection as this diplay type & `show\_as lines, selection\_name` \{\{nl\}\}`cmd.show\_as("lines", "selection\_name")` \tn 
% Row Count 4 (+ 4)
% Row 1
\SetRowColor{white}
add this display type of the selection & `show lines, selection\_name`\{\{nl\}\}`cmd.show("lines", "selection\_name")` \tn 
% Row Count 8 (+ 4)
% Row 2
\SetRowColor{LightBackground}
hide this display type of the selection & `hide lines, selection\_name`\{\{nl\}\}`cmd.hide("lines", "selection\_name")` \tn 
% Row Count 12 (+ 4)
% Row 3
\SetRowColor{white}
color the selection & `coloc color\_name, selection\_name` \tn 
% Row Count 14 (+ 2)
% Row 4
\SetRowColor{LightBackground}
zoom on the selection & zoom selection\_name \tn 
% Row Count 16 (+ 2)
\hhline{>{\arrayrulecolor{DarkBackground}}--}
\SetRowColor{LightBackground}
\mymulticolumn{2}{x{8.4cm}}{Show (S button) - Hide (H button) - Color (C button) \newline display type: lines, ribbon, cartoon, stick, label, nonbonded, mainchain, sidechain}  \tn 
\hhline{>{\arrayrulecolor{DarkBackground}}--}
\end{tabularx}
\par\addvspace{1.3em}

\begin{tabularx}{8.4cm}{x{7.12 cm} p{0.88 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{2}{x{8.4cm}}{\bf\textcolor{white}{Structure modification}}  \tn
% Row 0
\SetRowColor{LightBackground}
adds hydrogens in the appropriate places & h\_add \tn 
% Row Count 2 (+ 2)
\hhline{>{\arrayrulecolor{DarkBackground}}--}
\end{tabularx}
\par\addvspace{1.3em}

\begin{tabularx}{8.4cm}{x{4.72 cm} x{3.28 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{2}{x{8.4cm}}{\bf\textcolor{white}{get information}}  \tn
% Row 0
\SetRowColor{LightBackground}
count the number of atome of the selection & `count\_atoms \seqsplit{selection\_name`} \tn 
% Row Count 2 (+ 2)
\hhline{>{\arrayrulecolor{DarkBackground}}--}
\end{tabularx}
\par\addvspace{1.3em}

\begin{tabularx}{8.4cm}{x{4.104 cm} x{1.976 cm} x{1.52 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{3}{x{8.4cm}}{\bf\textcolor{white}{selection algebra}}  \tn
% Row 0
\SetRowColor{LightBackground}
Selects atoms that are not included in s1 & `not s1` & `! s1` \tn 
% Row Count 2 (+ 2)
% Row 1
\SetRowColor{white}
Selects atoms included in both s1 and s2 & `s1 and s2` & `s1 \& s2` \tn 
% Row Count 4 (+ 2)
% Row 2
\SetRowColor{LightBackground}
Selects atoms included in either s1 or s2 & `s1 or s2` & `s1 | s2` \tn 
% Row Count 6 (+ 2)
% Row 3
\SetRowColor{white}
Selects atoms in s1 whose identifiers name, resi, resn, chain and segi all match atoms in s2 & `s1 in s2` & `s1 in s2` \tn 
% Row Count 11 (+ 5)
% Row 4
\SetRowColor{LightBackground}
Selects atoms in s1 whose identifiers name and resi match atoms in s2 & `s1 like s2` & `s1 l. s2` \tn 
% Row Count 15 (+ 4)
% Row 5
\SetRowColor{white}
Selects all atoms whose van der Waals radii are separated from the van der Waals radii of s1 by a minimum of X Angstroms. & `s1 gap X` & `s1 gap X` \tn 
% Row Count 21 (+ 6)
% Row 6
\SetRowColor{LightBackground}
Selects atoms with centers within X Angstroms of the center of any atom in s1 & `s1 around X` & `s1 a. X` \tn 
% Row Count 25 (+ 4)
% Row 7
\SetRowColor{white}
Expands s1 by all atoms within X Angstroms of the center of any atom in s1 & `s1 expand X` & `s1 e. X` \tn 
% Row Count 29 (+ 4)
% Row 8
\SetRowColor{LightBackground}
Selects atoms in s1 that are within X Angstroms of the s2 & `s1 within X of s2` & `s1 w. X of s2` \tn 
% Row Count 32 (+ 3)
\end{tabularx}
\par\addvspace{1.3em}

\vfill
\columnbreak
\begin{tabularx}{8.4cm}{x{4.104 cm} x{1.976 cm} x{1.52 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{3}{x{8.4cm}}{\bf\textcolor{white}{selection algebra (cont)}}  \tn
% Row 9
\SetRowColor{LightBackground}
Expands selection to complete residues & `byres s1` & `br. s1` \tn 
% Row Count 2 (+ 2)
% Row 10
\SetRowColor{white}
Expands selection to complete objects & `byobject s1 ` & `bo. s1` \tn 
% Row Count 4 (+ 2)
% Row 11
\SetRowColor{LightBackground}
Selects atoms directly bonded to s1 & `neighbor s1` & `nbr. s1` \tn 
% Row Count 6 (+ 2)
\hhline{>{\arrayrulecolor{DarkBackground}}---}
\end{tabularx}
\par\addvspace{1.3em}


% That's all folks
\end{multicols*}

\end{document}