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updated texshade.sty; version number bumped to 1.23.1

UBodenhofer authored on 29/04/2021 12:32:02
Showing5 changed files

... ...
@@ -1,8 +1,8 @@
1 1
 Package: msa
2 2
 Type: Package
3 3
 Title: Multiple Sequence Alignment
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-Version: 1.23.0
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-Date: 2020-08-12
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+Version: 1.23.1
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+Date: 2021-04-29
6 6
 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7
 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
8 8
 Description: The 'msa' package provides a unified R/Bioconductor interface to
... ...
@@ -1,6 +1,18 @@
1 1
 Change history of package msa:
2 2
 ==============================
3 3
 
4
+Version 1.24.0:
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+- release as part of Bioconductor 3.13
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+
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+Version 1.23.1:
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+- updated texshade.sty to newest version
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+
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+Version 1.23.0:
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+- new branch for Bioconductor 3.13 devel
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+
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+Version 1.22.0:
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+- release as part of Bioconductor 3.12
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+
4 16
 Version 1.21.1:
5 17
 - changed msaClustalW() examples to run smoothly on Windows with R 4.0.x
6 18
 - added warning to msaClustalW() help page regarding cluster="upgma" on
7 19
new file mode 100644
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@@ -0,0 +1,19 @@
1
+
2
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3
+%%%%%                                                                      %%%%%
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+%%%%%            Ciliate macronuclear genetic code definitions             %%%%%
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+%%%%%                                                                      %%%%%
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+%%%%%    Only exchanges compared to the standard code must be defined.     %%%%%
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+%%%%%                                                                      %%%%%
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+%%%%%      (The last codon of the list is used for backtranslations        %%%%%
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+%%%%%       from protein to DNA sequences---therefore the wobbles)         %%%%%
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+%%%%%                                                                      %%%%%
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+%%%%%                                                                      %%%%%
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+%%%%%    Activate these definitions for your alignment by the following    %%%%%
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+%%%%%    command in the texshade environment:                              %%%%%
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+%%%%%                                                                      %%%%%
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+%%%%%                         \geneticcode{ciliate}                        %%%%%
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+%%%%%                                                                      %%%%%
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+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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+
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+\codon{Q}{TAA,TAG,UAA,UAG,YAR}
0 20
new file mode 100644
... ...
@@ -0,0 +1,34 @@
1
+
2
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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+%%%%%                                                                      %%%%%
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+%%%%%                   Standard genetic code definitions                  %%%%%
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+%%%%%                                                                      %%%%%
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+%%%%%      (The last codon of each list is used for backtranslations       %%%%%
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+%%%%%        from protein to DNA sequences---therefore the wobbles)        %%%%%
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+%%%%%                                                                      %%%%%
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+%%%%%              These definitions are default in TeXshade.              %%%%%
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+%%%%%     There is no need to load them. This is an example file only.     %%%%%
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+%%%%%                                                                      %%%%%
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+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
13
+
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+\codon{A}{GCA,GCG,GCC,GCT,GCU,GCN}
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+\codon{C}{TGC,TGT,UGC,UGU,TGY}
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+\codon{D}{GAC,GAT,GAU,GAY}
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+\codon{E}{GAA,GAG,GAR}
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+\codon{F}{TTC,TTT,UUC,UUU,TTY}
19
+\codon{G}{GGA,GGG,GGC,GGT,GGU,GGN}
20
+\codon{H}{CAC,CAT,CAY}
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+\codon{I}{ATA,ATC,ATT,AUA,AUC,AUU,ATH}
22
+\codon{K}{AAA,AAG,AAG,AAR}
23
+\codon{L}{CTA,CTG,CTC,CTT,TTA,TTG,CUG,CUG,CUC,CUU,UUA,UUG,YTN}
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+\codon{M}{ATG,AUG,ATG}
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+\codon{N}{AAC,AAT,AAU,AAY}
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+\codon{P}{CCA,CCG,CCC,CCT,CCU,CCN}
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+\codon{Q}{CAA,CAG,CAR}
28
+\codon{R}{AGA,AGG,CGA,CGG,CGC,CGT,CGU,MGN}
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+\codon{S}{TCT,TCC,TCG,TCA,AGT,AGC,UCU,UCC,UCG,UCA,AGU,WSN}
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+\codon{T}{ACT,ACC,ACG,ACA,ACU,ACN}
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+\codon{V}{GTA,GTG,GTC,GTT,GUA,GUG,GUC,GUU,GTN}
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+\codon{W}{TGG,UGG,TGG}
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+\codon{Y}{TAC,TAT,UAC,UAU,TAY}
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+\codon{.}{TAA,TAG,TGA,UAA,UAG,UGA,TRR}
... ...
@@ -8,13 +8,13 @@
8 8
 %% 
9 9
 %% LaTeX package for typesetting nucleotide and peptide alignments
10 10
 %% 
11
-%% Copyright (C) 1999-2011 Eric Beitz
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+%% Copyright (C) 1999-2021 Eric Beitz
12 12
 %% See the file texshade.txt
13 13
 %% 
14 14
 
15 15
 \NeedsTeXFormat{LaTeX2e}
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-\ProvidesPackage{texshade}[2011/05/13 LaTeX TeXshade (v1.24)]
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-\message{Package `texshade', Version 1.24 of 2011/12/01.}
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+\ProvidesPackage{texshade}[2021/04/01 LaTeX TeXshade (v1.26)]
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+\message{Package `texshade', Version 1.26 of 2021/04/01.}
18 18
 
19 19
 \PassOptionsToPackage{dvips}{color}
20 20
 \PassOptionsToPackage{dvips}{graphicx}
... ...
@@ -56,6 +56,7 @@
56 56
 \newread\structurefile  \newwrite\featurefile
57 57
 \newread\alignfile      \newread\sublogofile
58 58
 \newwrite\exp@rtfile
59
+\newwrite\exp@rt@chimerafile
59 60
 
60 61
 \expandafter\ifx\csname blacktriangleright\endcsname\relax
61 62
  \openin\structurefile = amssymb.sty
... ...
@@ -94,6 +95,7 @@
94 95
 \newlength\equal@height \newlength\temp@@length
95 96
 \newlength\vspace@legend
96 97
 \newlength\hspace@legend
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+\newlength\bar@length
97 99
 
98 100
 \newif\ifletter       \newif\ifnumber
99 101
 \newif\ifnewres       \newif\ifall@shade
... ...
@@ -678,6 +680,16 @@
678 680
 \xdef\HydroV{37}  \xdef\HydroW{28}  \xdef\HydroX{N}
679 681
 \xdef\HydroY{9}   \xdef\HydroZ{N}
680 682
 
683
+\xdef\hardnessA{98}  \xdef\hardnessB{0}   \xdef\hardnessC{37}
684
+\xdef\hardnessD{100} \xdef\hardnessE{96} \xdef\hardnessF{48}
685
+\xdef\hardnessG{92}  \xdef\hardnessH{50} \xdef\hardnessI{98}
686
+\xdef\hardnessJ{86}   \xdef\hardnessK{73} \xdef\hardnessL{98}
687
+\xdef\hardnessM{25}  \xdef\hardnessN{86} \xdef\hardnessO{0}
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+\xdef\hardnessP{91}   \xdef\hardnessQ{95} \xdef\hardnessR{69}
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+\xdef\hardnessS{94}  \xdef\hardnessT{98}  \xdef\hardnessU{-34}
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+\xdef\hardnessV{98}  \xdef\hardnessW{0}  \xdef\hardnessX{0}
691
+\xdef\hardnessY{28}   \xdef\hardnessZ{0}
692
+
681 693
 \xdef\consCB{0}  \xdef\consCJ{0}  \xdef\consCO{0}  \xdef\consCU{0}  \xdef\consCX{0}  \xdef\consCZ{0}
682 694
 \expandafter\xdef\csname consC?\endcsname{0}
683 695
 
... ...
@@ -2593,7 +2605,6 @@
2593 2605
             \expandafter\xdef\csname hide@@@seq\first@\endcsname{kill}
2594 2606
             \ifnum\first@=\cons@num \xdef\cons@num{0} \fi
2595 2607
             \advance\killseq@count by -1
2596
-            \seq@percent=100 \divide\seq@percent by \killseq@count
2597 2608
          \fi
2598 2609
       \fi\fi
2599 2610
       \xdef\first@{\first@@ @}
... ...
@@ -2612,7 +2623,6 @@
2612 2623
             \expandafter\xdef\csname hide@@@seq\fourth@\endcsname{kill}
2613 2624
             \ifnum\fourth@=\cons@num \xdef\cons@num{0} \fi
2614 2625
             \advance\killseq@count by -1
2615
-            \seq@percent=100 \divide\seq@percent by \killseq@count
2616 2626
          \fi
2617 2627
       \fi\fi
2618 2628
       \killseq@
... ...
@@ -2893,8 +2903,17 @@
2893 2903
       \funcgroup{Leu, Val, Ile}{LVI}{Green}{White}{upper}{up}
2894 2904
       \funcgroup{Pro}{P}{Apricot}{White}{upper}{up}
2895 2905
    \else
2906
+   \xdef\second@{hardness}
2907
+   \ifx\temp@\second@
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+      \funcgroup{22-23 eV (ADEGILPQSTV) | 2$\times$ HOMO-LUMO gap}{ADEGILPQSTV}{White}{BlueRed5}{upper}{up}
2909
+      \funcgroup{21-22 eV (KN)}{KN}{White}{BlueRed20}{upper}{up}
2910
+      \funcgroup{20-21 eV (R)}{R}{Black}{BlueRed40}{upper}{up}
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+      \funcgroup{19-20 eV (CFH)}{CFH}{Black}{BlueRed60}{upper}{up}
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+      \funcgroup{18-19 eV (MY)}{MY}{White}{BlueRed80}{upper}{up}
2913
+      \funcgroup{17-18 eV (W)}{W}{White}{BlueRed100}{upper}{up}
2914
+   \else
2896 2915
    \message{<Unknown shading mode - clearing `funcgroups'>}
2897
-   \fi\fi\fi\fi\fi\fi\fi
2916
+   \fi\fi\fi\fi\fi\fi\fi\fi
2898 2917
 }
2899 2918
 \def\shadeallresidues{\all@fshadetrue}
2900 2919
 \def\get@fromstack#1;#2;#3;#4;#5@{%
... ...
@@ -3114,22 +3133,33 @@
3114 3133
    \expandafter\xdef\csname stack@\bottop@\seq@\endcsname{\tmpstack}
3115 3134
 }
3116 3135
 \def\getarrow@shape#1#2#3#4&{%
3117
-   \xdef\first@@{#1}\xdef\second@@{#2}\xdef\third@@{#3}
3118
-   \if\first@@ v
3119
-      \if\second@@ =
3120
-      \else \xdef\style@{\first@@ v\third@@#4} \fi
3136
+   \xdef\first@@{#1}\xdef\second@@{#2}\xdef\third@@{#3}\xdef\fourth@@{#4}
3137
+   \ifx\temp@@\y@
3138
+      \if\first@@ ` \xdef\first@@{a} \else
3139
+      \if\first@@ ' \xdef\first@@{a} \else
3140
+      \if\first@@ , \xdef\first@@{b} \else
3141
+      \if\first@@ S \xdef\first@@{c} \xdef\second@@{-}
3142
+      \fi\fi\fi\fi
3143
+      \if\third@@ ` \xdef\third@@{a} \else
3144
+      \if\third@@ ' \xdef\third@@{a} \else
3145
+      \if\third@@ , \xdef\third@@{b} \else
3146
+      \if\third@@ S \xdef\third@@{c} \xdef\second@@{-}
3147
+      \fi\fi\fi\fi
3148
+      \xdef\style@{\first@@ -\third@@\fourth@@}
3149
+   \fi
3150
+   \if\first@@ S
3151
+      \xdef\style@{\first@@ -\third@@\fourth@@}
3121 3152
    \else
3122 3153
    \if\first@@ v
3123 3154
       \if\second@@ =
3124
-      \else \xdef\style@{\first@@ v\third@@#4} \fi
3155
+      \else \xdef\style@{\first@@ v\third@@\fourth@@} \fi
3125 3156
    \else
3126
-   \if\third@@ v
3127
-      \if\second@@ =
3128
-      \else \xdef\style@{\first@@ v\third@@#4} \fi
3157
+   \if\third@@ S
3158
+      \xdef\style@{\first@@ -\third@@\fourth@@}
3129 3159
    \else
3130 3160
    \if\third@@ v
3131 3161
       \if\second@@ =
3132
-      \else \xdef\style@{\first@@ v\third@@#4} \fi
3162
+      \else \xdef\style@{\first@@ v\third@@\fourth@@} \fi
3133 3163
    \fi\fi\fi\fi
3134 3164
 }
3135 3165
 \def\get@shape#1#2#3{%
... ...
@@ -5894,7 +5924,11 @@
5894 5924
          \fi
5895 5925
          \xdef\style@{cons[color]:cons[\f@color][0]}
5896 5926
       \else
5897
-         \xdef\style@{#4} \expandafter\getarrow@shape\temp@
5927
+         \xdef\style@{#4} \xdef\temp@@{n}
5928
+         \expandafter\get@firstfill\temp@
5929
+         \if\second@@ ^ \xdef\second@@{_} \fi
5930
+         \if\second@@ _ \xdef\temp@{\fill@char} \xdef\temp@@{y}\fi
5931
+         \expandafter\getarrow@shape\temp@
5898 5932
       \fi
5899 5933
       \fi
5900 5934
       \fi
... ...
@@ -6382,7 +6416,17 @@
6382 6416
       \logocolor{EQ}{RoyalPurple}
6383 6417
       \logocolor{R}{RedViolet}
6384 6418
       \logocolor{K}{Black}
6385
-   \fi\fi\fi\fi\fi\fi\fi
6419
+   \else
6420
+   \xdef\second@{hardness}
6421
+   \ifx\first@\second@
6422
+      \clearlogocolors
6423
+      \logocolor{ADEGILPQSTV}{BlueRed5}
6424
+      \logocolor{KN}{BlueRed20}
6425
+      \logocolor{R}{BlueRed40}
6426
+      \logocolor{CFH}{BlueRed60}
6427
+      \logocolor{MY}{BlueRed80}
6428
+      \logocolor{W}{BlueRed100}
6429
+   \fi\fi\fi\fi\fi\fi\fi\fi
6386 6430
 }
6387 6431
 \newcommand\findsubfamily[2][n]{%
6388 6432
    \xdef\first@{#1}
... ...
@@ -7793,9 +7837,8 @@
7793 7837
        \advance\pos@sum by 1 \fi
7794 7838
   \ifnum\innerloopcount<\seq@count \repeat
7795 7839
 
7796
-  \multiply\pos@sum by \seq@percent
7797 7840
   \expandafter\xdef\csname pos\the\loopcount\endcsname{\the\pos@sum}
7798
-  \expandafter\ifnum\csname pos\the\loopcount\endcsname<\thresh@ld
7841
+  \expandafter\ifnum\csname pos\the\loopcount\endcsname<\thresh@ld@
7799 7842
   \else
7800 7843
     \expandafter\ifnum\csname pos\the\loopcount\endcsname>\m@x
7801 7844
       \xdef\m@x{\csname pos\the\loopcount\endcsname}
... ...
@@ -7843,13 +7886,12 @@
7843 7886
   \expandafter\ifnum\csname pos\the\loopcount\endcsname=\seq@count
7844 7887
     \xdef\cons@seq{\the\loopcount} \xdef\match@case{2} \loopcount=1
7845 7888
   \else
7846
-   \multiply\pos@sum by \seq@percent
7847 7889
    \expandafter\xdef\csname pos\the\loopcount\endcsname{\the\pos@sum}
7848
-   \expandafter\ifnum\csname pos\the\loopcount\endcsname<\thresh@ld
7890
+   \expandafter\ifnum\csname pos\the\loopcount\endcsname<\thresh@ld@
7849 7891
    \else
7850 7892
     \expandafter\ifnum\csname pos\the\loopcount\endcsname>\m@x
7851 7893
       \xdef\m@x{\csname pos\the\loopcount\endcsname}
7852
-      \expandafter\ifnum\csname pos\the\loopcount\endcsname<\all@thresh@ld
7894
+      \expandafter\ifnum\csname pos\the\loopcount\endcsname<\all@thresh@ld@
7853 7895
          \xdef\cons@seq{\the\loopcount} \xdef\match@case{1}
7854 7896
       \else
7855 7897
          \xdef\cons@seq{\the\loopcount} \xdef\match@case{2}
... ...
@@ -10431,6 +10473,7 @@
10431 10473
              \fi
10432 10474
              \fi
10433 10475
              \expandafter\xdef\csname res@count\the\loopcount\endcsname{\the\res@count}
10476
+             \ifnum\loopcount=\chimera@seqnum \xdef\chimera@stack{\chimera@stack \the\res@count,} \fi
10434 10477
              \ifnum\loopcount=\exp@rt@num \xdef\sixth@{\the\res@count}\xdef\seventh@{y}\fi
10435 10478
              \ifnum\loopcount=\rule@num\relax
10436 10479
               \expandafter\ifnum\csname res@count\rule@num\endcsname>\rule@tens
... ...
@@ -10574,6 +10617,7 @@
10574 10617
                            \the\innerloopcount}
10575 10618
          \else
10576 10619
           \ifnum\loopcount=\rule@num \xdef\ruler@{\ruler@ -} \fi
10620
+          \ifnum\loopcount=\chimera@seqnum \xdef\chimera@stack{\chimera@stack &,} \fi
10577 10621
           \ifx\collect@valtop\yes
10578 10622
           \ifnum\v@lseqtop=\loopcount
10579 10623
              \xdef\v@ltop{\v@ltop,N}
... ...
@@ -11373,7 +11417,7 @@
11373 11417
          \textcolor{\legend@fg}{%
11374 11418
          \ifgerm@n\kern2ex\legend@size{nicht konserviert}%
11375 11419
          \else\ifsp@nish\kern2ex\legend@size{no conservado}%
11376
-         \else\kern2ex\legend@size{non conserved}\fi\fi}
11420
+         \else\kern2ex\legend@size{non-conserved}\fi\fi}
11377 11421
          \newline\hbox{}\noindent%
11378 11422
          \ifsimmode%
11379 11423
          \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi
... ...
@@ -11862,6 +11906,7 @@
11862 11906
 \def\get@tripletfill#1#2#3#4&{%
11863 11907
    \multiply\temp@count by -1%
11864 11908
    \def\second@@{#1}\def\second@@@{#2}\def\second@@@@{#3}\def\fill@char{#4&}}
11909
+
11865 11910
 \def\putfeature@style#1{%
11866 11911
    \residues@size%
11867 11912
    \setbox1=\hbox{\ensuremath{\overrightarrow{\hbox{}}}}%
... ...
@@ -11967,6 +12012,7 @@
11967 12012
        \fontseries{\featurestyles@series}%
11968 12013
        \fontshape{\featurestyles@shape}%
11969 12014
        \selectfont%
12015
+       \xdef\last@{bottom}%
11970 12016
        \ifx\bottop@\temp@\xdef\last@{0.35}\else\xdef\last@{0}\fi%
11971 12017
        \kern0.15\box@width%
11972 12018
        \loopcount=0\relax%
... ...
@@ -12137,6 +12183,7 @@
12137 12183
         \ifx\bottop@\temp@ \xdef\last@{0.35}\else\xdef\last@{-0.55}\fi%
12138 12184
         \textcolor{\f@color}{%
12139 12185
         \raisebox{\last@\arrow@height}{%
12186
+         \if\first@@ b \xdef\first@@{,}\fi%
12140 12187
          \if\first@@ ,%
12141 12188
             \rule{0.1\arrow@height}{\arrow@height}\kern-0.35\arrow@height%
12142 12189
          \else%
... ...
@@ -12144,6 +12191,10 @@
12144 12191
                \rule{0.1\arrow@height}{2\arrow@height}\kern-0.35\arrow@height%
12145 12192
             \else%
12146 12193
                \if\first@@ `\xdef\first@@{'}\fi%
12194
+               \if\first@@ '%
12195
+                  \rule[\arrow@height]%
12196
+                     {0.1\arrow@height}{\arrow@height}\kern-0.35\arrow@height%
12197
+               \else%
12147 12198
                \if\first@@ '%
12148 12199
                   \rule[\arrow@height]%
12149 12200
                      {0.1\arrow@height}{\arrow@height}\kern-0.35\arrow@height%
... ...
@@ -12152,6 +12203,7 @@
12152 12203
                      \rule{0pt}{0pt}\kern-0.35\arrow@height%
12153 12204
                   \fi%
12154 12205
                \fi%
12206
+               \fi%
12155 12207
             \fi%
12156 12208
          \fi%
12157 12209
          \if\third@@ v%
... ...
@@ -12212,6 +12264,7 @@
12212 12264
                  \xdef\last@{-0.25}\fi\fi\fi\fi%
12213 12265
         \textcolor{\f@color}{%
12214 12266
         \raisebox{\last@\arrow@height}{%
12267
+         \if\first@@ b \xdef\first@@{,}\fi%
12215 12268
          \if\first@@ ,%
12216 12269
             \rule[-0.5\arrow@height]{0.1\arrow@height}{1.5\arrow@height}%
12217 12270
             \kern-0.1\arrow@height%
... ...
@@ -12220,7 +12273,8 @@
12220 12273
                \rule[-0.5\arrow@height]{0.1\arrow@height}{2.25\arrow@height}%
12221 12274
                \kern-0.1\arrow@height%
12222 12275
             \else%
12223
-               \if\first@@ `\xdef\first@@{'}\fi%
12276
+               \if\first@@ a \xdef\first@@{'}\fi%
12277
+               \if\first@@ ` \xdef\first@@{'}\fi%
12224 12278
                \if\first@@ '%
12225 12279
                   \rule[0.4\arrow@height]%
12226 12280
                      {0.1\arrow@height}{1.5\arrow@height}%
... ...
@@ -12245,6 +12299,7 @@
12245 12299
             \rule[0.37\arrow@height]{\width@tmp}{0.1\arrow@height}%
12246 12300
             \kern-\width@tmp%
12247 12301
             \rule[0.9\arrow@height]{\width@tmp}{0.1\arrow@height}%
12302
+            \if\first@@ b \xdef\first@@{,}\fi%
12248 12303
             \if\third@@ ,%
12249 12304
                \kern-0.05\arrow@height%
12250 12305
                \rule[-0.5\arrow@height]{0.1\arrow@height}{1.5\arrow@height}%
... ...
@@ -12253,10 +12308,16 @@
12253 12308
                   \kern-0.05\arrow@height%
12254 12309
                   \rule[-0.5\arrow@height]{0.1\arrow@height}{2.25\arrow@height}%
12255 12310
                \else%
12256
-                  \if\third@@ `\xdef\third@@{'}\fi%
12311
+                  \if\first@@ a \xdef\first@@{'}\fi%
12312
+                  \if\third@@ ` \xdef\third@@{'}\fi%
12257 12313
                   \if\third@@ '%
12258 12314
                      \kern-0.05\arrow@height%
12259 12315
                      \rule[0.4\arrow@height]{0.1\arrow@height}{1.5\arrow@height}%
12316
+                  \else%
12317
+                  \if\third@@ a%
12318
+                     \kern-0.05\arrow@height%
12319
+                     \rule[0.4\arrow@height]{0.1\arrow@height}{1.5\arrow@height}%
12320
+                  \fi%
12260 12321
                   \fi%
12261 12322
                \fi%
12262 12323
             \fi%
... ...
@@ -12268,9 +12329,25 @@
12268 12329
         \advance\width@tmp by -0.5\temp@@length%
12269 12330
         \if\first@@ o\xdef\first@@{O}\fi%
12270 12331
         \if\third@@ o\xdef\third@@{O}\fi%
12332
+        \xdef\last@{bottom}%
12333
+        \ifx\fe@turep@s\last@%
12334
+           \vspace{-20pt}\message{(((-20pt)))}%
12335
+        \fi%
12271 12336
         \textcolor{\f@color}{%
12272 12337
          \if\first@@ ,%
12273
-         \rule{\temp@@length}{\arrow@height}\kern-\temp@@length%
12338
+           \rule{\temp@@length}{\arrow@height}\kern-\temp@@length%
12339
+         \else%
12340
+         \if\first@@ b%
12341
+           \xdef\last@{bottom}%
12342
+           \ifx\fe@turep@s\last@%
12343
+            \rule{\temp@@length}{\arrow@height}\kern-\temp@@length%
12344
+           \else
12345
+            \xdef\shift@feature{y}%
12346
+            \kern-\temp@@length%
12347
+            \rule[-\bar@length]{\temp@@length}{\bar@length}%
12348
+            \kern-\temp@@length%
12349
+            \rule{\temp@@length}{\arrow@height}\kern-\temp@@length%
12350
+           \fi
12274 12351
          \else%
12275 12352
             \if\first@@ |%
12276 12353
                \rule{\temp@@length}{2\arrow@height}\kern-\temp@@length%
... ...
@@ -12278,6 +12355,52 @@
12278 12355
               \if\first@@ O%
12279 12356
                 \raisebox{0.06ex}{\ensuremath{\bullet}}\kern-0.55ex%
12280 12357
                 \rule[\width@tmp]{0.65ex}{\temp@@length}%
12358
+              \else%
12359
+              \if\first@@ S%
12360
+                \xdef\last@{bottom}%
12361
+                \ifx\fe@turep@s\last@%
12362
+                   \advance\width@tmp by 0.5\temp@@length%
12363
+                   \kern0.5\box@width%
12364
+                   \kern-2\temp@@length%
12365
+                   \rule[\width@tmp]{\temp@@length}{\arrow@height}%
12366
+                   \advance\width@tmp by -0.5\temp@@length%
12367
+                   \kern-\temp@@length%
12368
+                   \rule[\width@tmp]{0.5\temp@@length}{\temp@@length}%
12369
+                   \rule[\width@tmp]{0.5\box@width}{\temp@@length}%
12370
+                \else%
12371
+                   \kern0.5\box@width%
12372
+                   \kern-2\temp@@length%
12373
+                   \rule{\temp@@length}{\arrow@height}%
12374
+                   \kern-\temp@@length%
12375
+                   \rule[\width@tmp]{0.5\temp@@length}{\temp@@length}%
12376
+                   \rule[\width@tmp]{0.5\box@width}{\temp@@length}%
12377
+                \fi%
12378
+              \else%
12379
+              \if\first@@ c%
12380
+                \xdef\last@{bottom}%
12381
+                \ifx\fe@turep@s\last@%
12382
+                   \advance\width@tmp by 0.5\temp@@length%
12383
+                   \raisebox{\arrow@height}{\rule[\box@height]{0pt}{\bar@length}}%%%%%%%%%%%%%%%%%%%%%%%
12384
+                   \kern0.5\box@width%
12385
+                   \kern-2\temp@@length%
12386
+                   \rule[2\arrow@height]{\temp@@length}{\bar@length}%%%%%%%%%%%%%%%%%%%%%%
12387
+                   \kern-\temp@@length%%%%%%%%%%%%%%%%%%%%%%%%%
12388
+                   \rule[\width@tmp]{\temp@@length}{\arrow@height}%
12389
+                   \advance\width@tmp by -0.5\temp@@length%
12390
+                   \kern-\temp@@length%
12391
+                   \rule[\width@tmp]{0.5\temp@@length}{\temp@@length}%
12392
+                   \rule[\width@tmp]{0.5\box@width}{\temp@@length}%
12393
+                \else%
12394
+                   \xdef\shift@feature{y}%
12395
+                   \kern0.5\box@width%
12396
+                   \kern-2\temp@@length%
12397
+                   \rule[-\bar@length]{\temp@@length}{\bar@length}%
12398
+                   \kern-\temp@@length%
12399
+                   \rule{\temp@@length}{\arrow@height}%
12400
+                   \kern-\temp@@length%
12401
+                   \rule[\width@tmp]{0.5\temp@@length}{\temp@@length}%
12402
+                   \rule[\width@tmp]{0.5\box@width}{\temp@@length}%
12403
+                \fi%
12281 12404
               \else%
12282 12405
                \if\first@@ <%
12283 12406
                  \raisebox{0.06ex}{\ensuremath{\blacktriangleleft}}\kern-0.35ex%
... ...
@@ -12290,13 +12413,20 @@
12290 12413
                 \fi%
12291 12414
                \fi%
12292 12415
               \fi%
12416
+              \fi%
12417
+              \fi%
12293 12418
             \fi%
12294 12419
          \fi%
12420
+         \fi%
12295 12421
          \loopcount=\second@%
12296 12422
          \if\first@@ <\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi%
12297 12423
          \if\third@@ >\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi%
12298 12424
          \if\first@@ O\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi%
12299 12425
          \if\third@@ O\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi%
12426
+         \if\first@@ S\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi%
12427
+         \if\third@@ S\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi%
12428
+         \if\first@@ c\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi%
12429
+         \if\third@@ c\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi%
12300 12430
          \xdef\second@{\the\loopcount}%
12301 12431
          \rule[\width@tmp]{\second@\box@width}{\temp@@length}%
12302 12432
          \setbox1=\hbox{\residues@size{\fill@char}}%
... ...
@@ -12306,6 +12436,17 @@
12306 12436
          \hbox to \second@\box@width{\textcolor{\frame@color}{\residues@size{\hss\fill@char\hss}}}%
12307 12437
          \if\third@@ ,%
12308 12438
          \kern-\temp@@length\rule{\temp@@length}{\arrow@height}%
12439
+         \else%
12440
+         \if\third@@ b%
12441
+           \xdef\last@{bottom}%
12442
+           \ifx\fe@turep@s\last@%
12443
+            \kern-\temp@@length\rule{\temp@@length}{\arrow@height}%
12444
+           \else
12445
+            \xdef\shift@feature{y}%
12446
+            \kern-\temp@@length%
12447
+            \rule[-\bar@length]{\temp@@length}{\bar@length}%
12448
+            \kern-\temp@@length\rule{\temp@@length}{\arrow@height}%
12449
+           \fi
12309 12450
          \else%
12310 12451
             \if\third@@ |%
12311 12452
                \kern-\temp@@length\rule{\temp@@length}{2\arrow@height}%
... ...
@@ -12313,6 +12454,31 @@
12313 12454
               \if\third@@ O%
12314 12455
                 \rule[\width@tmp]{0.65ex}{\temp@@length}%
12315 12456
                 \kern-0.55ex\raisebox{0.06ex}{\ensuremath{\bullet}}%
12457
+              \else%
12458
+              \if\third@@ S%
12459
+                \rule[\width@tmp]{0.5\box@width}{\temp@@length}%
12460
+                \rule[\width@tmp]{0.5\temp@@length}{\temp@@length}%
12461
+                \xdef\last@{bottom}%
12462
+                \ifx\fe@turep@s\last@%
12463
+                  \advance\width@tmp by 0.5\temp@@length%
12464
+                  \kern-\temp@@length\rule[\width@tmp]{\temp@@length}{\arrow@height}%
12465
+                \else
12466
+                  \kern-\temp@@length\rule{\temp@@length}{\arrow@height}%
12467
+                \fi%
12468
+              \else%
12469
+              \if\third@@ c%
12470
+                \xdef\shift@feature{y}%
12471
+                \rule[\width@tmp]{0.5\box@width}{\temp@@length}%
12472
+                \xdef\last@{bottom}%
12473
+                \ifx\fe@turep@s\last@%
12474
+                  \kern-\temp@@length%%%%%%%%%%%%%%%%%%%%%%%%%
12475
+                  \rule[2\arrow@height]{\temp@@length}{\bar@length}%%%%%%%%%%%%%%%%%%%%%%
12476
+                  \advance\width@tmp by 0.5\temp@@length%
12477
+                  \kern-\temp@@length\rule[\width@tmp]{\temp@@length}{\arrow@height}%
12478
+                \else
12479
+                  \kern-\temp@@length\rule[-\bar@length]{\temp@@length}{\bar@length}%
12480
+                  \kern-\temp@@length\rule{\temp@@length}{\arrow@height}%
12481
+                \fi%
12316 12482
               \else%
12317 12483
                \if\third@@ >%
12318 12484
                 \kern-0.35ex\raisebox{0.06ex}{\ensuremath{\blacktriangleright}}%
... ...
@@ -12324,7 +12490,10 @@
12324 12490
                 \fi%
12325 12491
                \fi%
12326 12492
               \fi%
12327
-            \fi
12493
+              \fi%
12494
+              \fi%
12495
+            \fi%
12496
+         \fi%
12328 12497
          \fi}%
12329 12498
        \fi
12330 12499
       \fi
... ...
@@ -12731,9 +12900,550 @@
12731 12900
    \divide\loopcount by 100 %
12732 12901
    \xdef\third@{\the\loopcount}%
12733 12902
 }
12903
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
12904
+%%%%                         Chimera export routines                      %%%%
12905
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
12906
+\def\chimeraballScale#1{\xdef\chimerab@llSc@le{#1}}
12907
+\def\chimeraballscale#1{\xdef\chimerab@llSc@le{#1}}
12908
+\def\chimeraaxisdistance#1#2#3{\xdef\chimera@xdist@nce{#1}\xdef\chimera@ydist@nce{#2}\xdef\chimera@zdist@nce{#3}}
12909
+\def\memelabelcutoff#1{%
12910
+   \xdef\label@threshold@lower{#1}
12911
+   \setlength\temp@@length{1000sp}
12912
+   \setlength\temp@@length{\label@threshold@lower\temp@@length}
12913
+   \loopcount=\temp@@length
12914
+   \xdef\label@threshold@lowerIOOO{\the\loopcount}
12915
+   \xdef\label@threshold@lowerremainingIOOO{-\the\loopcount}
12916
+}
12917
+\def\chimera@color@get#1#2@{%
12918
+   \xdef\first@{#1}\xdef\third@{#2@}
12919
+   \ifx\first@\ampers@nd
12920
+   \else
12921
+      \ifnum`#1>96 \make@upper\fi
12922
+      \if\second@ O \else \expandafter\xdef\csname chimera@col@\first@\endcsname{\second@} \fi
12923
+      \expandafter\chimera@color@get\third@
12924
+   \fi
12925
+}
12926
+\def\memered#1{%
12927
+      \xdef\third@{#1&@}
12928
+      \xdef\second@{red}
12929
+      \expandafter\chimera@color@get\third@
12930
+}
12931
+\def\memeblue#1{%
12932
+      \xdef\third@{#1&@}
12933
+      \xdef\second@{blue}
12934
+      \expandafter\chimera@color@get\third@
12935
+}
12936
+\def\memeyellow#1{%
12937
+      \xdef\third@{#1&@}
12938
+      \xdef\second@{yellow}
12939
+      \expandafter\chimera@color@get\third@
12940
+}
12941
+\def\memeblack#1{%
12942
+      \xdef\third@{#1&@}
12943
+      \xdef\second@{black}
12944
+      \expandafter\chimera@color@get\third@
12945
+}
12946
+\def\memewhite#1{%
12947
+      \xdef\third@{#1&@}
12948
+      \xdef\second@{white}
12949
+      \expandafter\chimera@color@get\third@
12950
+}
12951
+\def\memenone#1{%
12952
+      \xdef\third@{#1&@}
12953
+      \xdef\second@{none}
12954
+      \expandafter\chimera@color@get\third@
12955
+}
12956
+\def\memeRed#1{\memered{#1}}
12957
+\def\memeBlue#1{\memeblue{#1}}
12958
+\def\memeYellow#1{\memeyellow{#1}}
12959
+\def\memeBlack#1{\memeblack{#1}}
12960
+\def\memeWhite#1{\memewhite{#1}}
12961
+\def\memeNone#1{\memenone{#1}}
12962
+\def\chimera@colors#1#2@{%
12963
+   \xdef\first@{#1}\xdef\third@{#2@}
12964
+   \ifx\first@\ampers@nd
12965
+   \else
12966
+      \xdef\second@{\csname chimera@col@\first@\endcsname}
12967
+      \expandafter\xdef\csname chimera@list@\second@\endcsname{\csname chimera@list@\second@\endcsname \first@}
12968
+      \expandafter\chimera@colors\third@
12969
+   \fi
12970
+}
12971
+\def\memeStandardcolors{%
12972
+   \xdef\chimera@col@A{white}
12973
+   \xdef\chimera@col@B{none}
12974
+   \xdef\chimera@col@C{yellow}
12975
+   \xdef\chimera@col@D{red}
12976
+   \xdef\chimera@col@E{red}
12977
+   \xdef\chimera@col@F{black}
12978
+   \xdef\chimera@col@G{yellow}
12979
+   \xdef\chimera@col@H{blue}
12980
+   \xdef\chimera@col@I{black}
12981
+   \xdef\chimera@col@J{none}
12982
+   \xdef\chimera@col@K{blue}
12983
+   \xdef\chimera@col@L{black}
12984
+   \xdef\chimera@col@M{black}
12985
+   \xdef\chimera@col@N{yellow}
12986
+   \xdef\chimera@col@O{none}
12987
+   \xdef\chimera@col@P{white}
12988
+   \xdef\chimera@col@Q{yellow}
12989
+   \xdef\chimera@col@R{blue}
12990
+   \xdef\chimera@col@S{yellow}
12991
+   \xdef\chimera@col@T{yellow}
12992
+   \xdef\chimera@col@U{none}
12993
+   \xdef\chimera@col@V{white}
12994
+   \xdef\chimera@col@W{black}
12995
+   \xdef\chimera@col@X{none}
12996
+   \xdef\chimera@col@Y{yellow}
12997
+   \xdef\chimera@col@Z{none}
12998
+}
12999
+\def\echostructurefile#1{\xdef\echo@filename{, e.g. #1}}
13000
+\def\chimerachain#1{\xdef\chimerach@in{.#1}}
13001
+\catcode`\"=6 \catcode`\#=12 \catcode`\~=12
13002
+\newcommand{\structurememe}[2][chimera.cmd]{%
13003
+   \ifx\exp@rt@chimera\n@
13004
+      \xdef\first@{"2 @} \expandafter\check@letter\first@
13005
+      \xdef\first@{"2}   \ifletter \get@name@number \fi
13006
+      \xdef\chimera@seqnum{\first@}
13007
+      \xdef\exp@rt@chimera{y}
13008
+      \xdef\first@{"1}
13009
+      \immediate\openout\exp@rt@chimerafile = \first@
13010
+   \fi
13011
+}
13012
+\def\init@chimera@file{%
13013
+      \xdef\chimera@list@red{} \xdef\chimera@list@blue{} \xdef\chimera@list@yellow{} \xdef\chimera@list@black{} \xdef\chimera@list@white{}
13014
+      \xdef\chimera@list@none{}
13015
+      \xdef\first@{ABCDEFGHIJKLMNOPQRSTUVWXYZ&@}
13016
+      \expandafter\chimera@colors\first@
13017
+      \immediate\write\exp@rt@chimerafile{############################################################}
13018
+      \immediate\write\exp@rt@chimerafile{###}
13019
+      \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }. O � o STRUCTURE MEME � . O o}
13020
+      \immediate\write\exp@rt@chimerafile{###}
13021
+      \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }Chimera command file generated from TeXshade logo data}
13022
+      \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }use '.cmd' or '.com' suffix}
13023
+      \immediate\write\exp@rt@chimerafile{###}
13024
+      \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }Reference sequence: '\csname newseqname\chimera@seqnum\endcsname'\echo@filename}
13025
+      \immediate\write\exp@rt@chimerafile{###}
13026
+      \immediate\write\exp@rt@chimerafile{############################################################}
13027
+      \immediate\write\exp@rt@chimerafile{}
13028
+      \immediate\write\exp@rt@chimerafile{############################################################}
13029
+      \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }residue colors: (set with \string\memeRed{residues}\unexpanded{ }etc.)}
13030
+      \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\chimera@list@red \unexpanded{ }(Red)}
13031
+      \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\chimera@list@blue \unexpanded{ }(Blue)}
13032
+      \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\chimera@list@yellow \unexpanded{ }(Yellow)}
13033
+      \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\chimera@list@black \unexpanded{ }(Black)}
13034
+      \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\chimera@list@white \unexpanded{ }(White)}
13035
+      \immediate\write\exp@rt@chimerafile{############################################################}
13036
+      \immediate\write\exp@rt@chimerafile{}
13037
+      \immediate\write\exp@rt@chimerafile{############################################################}
13038
+      \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }residues in labels: (\string\memelabelcutoff{bit-value})}
13039
+      \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\label@threshold@lower\unexpanded{ }bit required to appear}
13040
+      \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }> : . indicate 3, 2, and 1 bit levels}
13041
+      \immediate\write\exp@rt@chimerafile{############################################################}
13042
+      \immediate\write\exp@rt@chimerafile{}
13043
+      \immediate\write\exp@rt@chimerafile{############################################################}
13044
+      \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }initialize & load structure}
13045
+      \immediate\write\exp@rt@chimerafile{############################################################}
13046
+      \immediate\write\exp@rt@chimerafile{close session; background solid white;}
13047
+      \immediate\write\exp@rt@chimerafile{echo load structure file for '\csname newseqname\chimera@seqnum\endcsname'\echo@filename}
13048
+      \immediate\write\exp@rt@chimerafile{open #0; ~ribbon; ~surface}
13049
+      \immediate\write\exp@rt@chimerafile{}
13050
+      \immediate\write\exp@rt@chimerafile{############################################################}
13051
+      \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }to set ball scale, change factor ]0.0 - 1.0]}
13052
+      \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }in 'setattr m ballScale <factor> #0' below,}
13053
+      \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }or use the \string\chimeraballScale{factor}\unexpanded{ }command}
13054
+      \immediate\write\exp@rt@chimerafile{############################################################}
13055
+      \immediate\write\exp@rt@chimerafile{setattr m ballScale \chimerab@llSc@le \unexpanded{ }#0}
13056
+      \immediate\write\exp@rt@chimerafile{}
13057
+      \immediate\write\exp@rt@chimerafile{############################################################}
13058
+      \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }display alpha-carbons only}
13059
+      \immediate\write\exp@rt@chimerafile{############################################################}
13060
+      \immediate\write\exp@rt@chimerafile{represent bs @ca; show @ca}
13061
+      \immediate\write\exp@rt@chimerafile{}
13062
+      \ifshow@sublogo
13063
+            \immediate\write\exp@rt@chimerafile{############################################################}
13064
+            \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }duplicate structure;}
13065
+            \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }to alter direction or Angstrom distance, set}
13066
+            \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }'move <x, y, or z> 1 <distance> models #1' below,}
13067
+            \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }or use the \string\chimeraaxisdistance{x}{y}{z}\unexpanded{ }command}
13068
+            \immediate\write\exp@rt@chimerafile{############################################################}
13069
+            \immediate\write\exp@rt@chimerafile{combine #0}
13070
+            \ifnum\chimera@xdist@nce>0
13071
+               \immediate\write\exp@rt@chimerafile{move x 1 \chimera@xdist@nce \unexpanded{ }models #1}
13072
+            \fi
13073
+            \ifnum\chimera@ydist@nce>0
13074
+               \immediate\write\exp@rt@chimerafile{move y 1 \chimera@ydist@nce \unexpanded{ }models #1}
13075
+            \fi
13076
+            \ifnum\chimera@zdist@nce>0
13077
+               \immediate\write\exp@rt@chimerafile{move z 1 \chimera@zdist@nce \unexpanded{ }models #1}
13078
+            \fi
13079
+            \immediate\write\exp@rt@chimerafile{}
13080
+            \immediate\write\exp@rt@chimerafile{############################################################}
13081
+            \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }focus view and name structure models}
13082
+            \immediate\write\exp@rt@chimerafile{############################################################}
13083
+            \immediate\write\exp@rt@chimerafile{wait; focus #0#1}
13084
+            \ifx\sublogo@name@user\ampers@nd
13085
+                \immediate\write\exp@rt@chimerafile{setattr m name subfamily #0}
13086
+            \else
13087
+                \immediate\write\exp@rt@chimerafile{setattr m name '\sublogo@name@user' \unexpanded{ }#0}
13088
+            \fi
13089
+            \xdef\first@{\sublogo@name@neg &}
13090
+            \ifx\first@\ampers@nd
13091
+                \immediate\write\exp@rt@chimerafile{setattr m name remaining #1}
13092
+            \else
13093
+                \immediate\write\exp@rt@chimerafile{setattr m name '\sublogo@name@neg' \unexpanded{ }#1}
13094
+            \fi
13095
+     \else
13096
+            \immediate\write\exp@rt@chimerafile{\string ############################################################}
13097
+            \immediate\write\exp@rt@chimerafile{\string ###\unexpanded{ }\unexpanded{ }\unexpanded{ }name structure model}
13098
+            \immediate\write\exp@rt@chimerafile{\string ############################################################}
13099
+            \ifx\logo@name@user\ampers@nd
13100
+                \immediate\write\exp@rt@chimerafile{setattr m name logo #0}
13101
+            \else
13102
+                \immediate\write\exp@rt@chimerafile{setattr m name '\logo@name@user' \unexpanded{ }#0}
13103
+            \fi
13104
+      \fi
13105
+      \immediate\write\exp@rt@chimerafile{}
13106
+      \immediate\write\exp@rt@chimerafile{############################################################}
13107
+      \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }logo data}
13108
+      \immediate\write\exp@rt@chimerafile{############################################################}
13109
+}
13110
+\def\make@HEX{%
13111
+     \xdef\sixth@{\the\loopcount}%
13112
+     \divide\loopcount by 4096\relax%
13113
+     \ifnum\loopcount=10\relax%
13114
+        \xdef\seventh@{A}%
13115
+     \else%
13116
+     \ifnum\loopcount=11\relax%
13117
+        \xdef\seventh@{B}%
13118
+     \else%
13119
+     \ifnum\loopcount=12\relax%
13120
+        \xdef\seventh@{C}%
13121
+     \else%
13122
+     \ifnum\loopcount=13\relax%
13123
+        \xdef\seventh@{D}%
13124
+     \else%
13125
+     \ifnum\loopcount=14\relax%
13126
+        \xdef\seventh@{E}%
13127
+     \else%
13128
+     \ifnum\loopcount>14\relax%
13129
+        \xdef\seventh@{F}%
13130
+     \else%
13131
+        \xdef\seventh@{\the\loopcount}%
13132
+     \fi\fi\fi\fi\fi\fi%
13133
+     \multiply\loopcount by -4096\relax%
13134
+     \advance\loopcount by \sixth@%
13135
+     \xdef\sixth@{\the\loopcount}%
13136
+     \divide\loopcount by 256\relax%
13137
+     \ifnum\loopcount=10 \relax%
13138
+        \xdef\eighth@{A}%
13139
+     \else%
13140
+     \ifnum\loopcount=11 \relax%
13141
+        \xdef\eighth@{B}%
13142
+     \else%
13143
+     \ifnum\loopcount=12 \relax%
13144
+        \xdef\eighth@{C}%
13145
+     \else%
13146
+     \ifnum\loopcount=13 \relax%
13147
+        \xdef\eighth@{D}%
13148
+     \else%
13149
+     \ifnum\loopcount=14 \relax%
13150
+        \xdef\eighth@{E}%
13151
+     \else%
13152
+     \ifnum\loopcount>14 \relax%
13153
+        \xdef\eighth@{F}%
13154
+     \else%
13155
+        \xdef\eighth@{\the\loopcount}%
13156
+     \fi\fi\fi\fi\fi\fi%
13157
+     \xdef\seventh@{\seventh@\eighth@}%
13158
+     \multiply\loopcount by -256\relax%
13159
+     \advance\loopcount by \sixth@%
13160
+     \xdef\sixth@{\the\loopcount}%
13161
+     \divide\loopcount by 16\relax%
13162
+     \ifnum\loopcount=10\relax%
13163
+        \xdef\eighth@{A}%
13164
+     \else%
13165
+     \ifnum\loopcount=11\relax%
13166
+        \xdef\eighth@{B}%
13167
+     \else%
13168
+     \ifnum\loopcount=12\relax%
13169
+        \xdef\eighth@{C}%
13170
+     \else%
13171
+     \ifnum\loopcount=13\relax%
13172
+        \xdef\eighth@{D}%
13173
+     \else%
13174
+     \ifnum\loopcount=14\relax%
13175
+        \xdef\eighth@{E}%
13176
+     \else%
13177
+     \ifnum\loopcount>14\relax%
13178
+        \xdef\eighth@{F}%
13179
+     \else%
13180
+        \xdef\eighth@{\the\loopcount}%
13181
+     \fi\fi\fi\fi\fi\fi%
13182
+     \xdef\seventh@{\seventh@\eighth@}%
13183
+     \multiply\loopcount by -16\relax%
13184
+     \advance\loopcount by \sixth@\relax%
13185
+     \ifnum\loopcount=10\relax%
13186
+        \xdef\eighth@{A}%
13187
+     \else%
13188
+     \ifnum\loopcount=11\relax%
13189
+        \xdef\eighth@{B}%
13190
+     \else%
13191
+     \ifnum\loopcount=12\relax%
13192
+        \xdef\eighth@{C}%
13193
+     \else%
13194
+     \ifnum\loopcount=13\relax%
13195
+        \xdef\eighth@{D}%
13196
+     \else%
13197
+     \ifnum\loopcount=14\relax%
13198
+        \xdef\eighth@{E}%
13199
+     \else%
13200
+     \ifnum\loopcount>14\relax%
13201
+        \xdef\eighth@{F}%
13202
+     \else%
13203
+        \xdef\eighth@{\the\loopcount}%
13204
+     \fi\fi\fi\fi\fi\fi%
13205
+     \xdef\seventh@{\seventh@\eighth@}%
13206
+}
13207
+\def\write@chimera@data{%
13208
+      \ifnum\temp@count>0 \else\temp@count=1\relax\temp@@count=0\fi%
13209
+      \loopcount=\temp@count%
13210
+      \xdef\fourth@{\the\loopcount @}%
13211
+      \ifnum\loopcount>9999 \expandafter\decimal@A\fourth@ \else%
13212
+      \ifnum\loopcount>999  \expandafter\decimal@B\fourth@ \else%
13213
+      \ifnum\loopcount>99   \expandafter\decimal@C\fourth@ \else%
13214
+      \ifnum\loopcount>9    \expandafter\decimal@D\fourth@ \else%
13215
+                            \expandafter\decimal@E\fourth@%
13216
+      \fi\fi\fi\fi%
13217
+      \loopcount=\chimera@subfamily@col@black%
13218
+      \multiply\loopcount by 65535\relax%
13219
+      \divide\loopcount by \temp@count%
13220
+      \xdef\chimera@subfamily@col@black{\the\loopcount}%
13221
+      \loopcount=65535\relax%
13222
+      \advance\loopcount by -\chimera@subfamily@col@black%
13223
+      \xdef\temp@@{\the\loopcount}%
13224
+%%%%%%%%%%%%%%
13225
+%%%%%%%%%%%%%%
13226
+      \loopcount=\chimera@subfamily@col@blue\relax%
13227
+      \ifnum\chimera@subfamily@col@yellow>\loopcount\relax%
13228
+         \loopcount=\chimera@subfamily@col@yellow\relax%
13229
+      \else%
13230
+         \ifnum\chimera@subfamily@col@red>\loopcount\relax%
13231
+            \loopcount=\chimera@subfamily@col@red\relax%
13232
+         \fi%
13233
+      \fi%
13234
+      \xdef\max@yellow{\the\loopcount}%
13235
+      \ifnum\chimera@subfamily@col@blue<\chimera@subfamily@col@yellow\relax%
13236
+         \xdef\chimera@subfamily@col@green{\chimera@subfamily@col@blue}%
13237
+      \else%
13238
+         \xdef\chimera@subfamily@col@green{\chimera@subfamily@col@yellow}%
13239
+      \fi%
13240
+      \loopcount=\chimera@subfamily@col@yellow\relax%
13241
+      \advance\loopcount by -\chimera@subfamily@col@green%
13242
+      \xdef\chimera@subfamily@col@yellow{\the\loopcount}%
13243
+      \loopcount=\chimera@subfamily@col@blue\relax%
13244
+      \advance\loopcount by -\chimera@subfamily@col@green%
13245
+      \xdef\chimera@subfamily@col@blue{\the\loopcount}%
13246
+      \ifnum\chimera@subfamily@col@blue>0\relax%
13247
+         \ifnum\chimera@subfamily@col@green>0\relax%
13248
+            \loopcount=\chimera@subfamily@col@blue\relax%
13249
+            \multiply\loopcount by 2\relax \xdef\chimera@subfamily@col@blue{\the\loopcount}%
13250
+            \loopcount=\chimera@subfamily@col@green\relax%
13251
+            \multiply\loopcount by 2\relax \xdef\chimera@subfamily@col@green{\the\loopcount}%
13252
+         \fi%
13253
+      \fi%
13254
+      \loopcount=\chimera@subfamily@col@green\relax%
13255
+      \advance\loopcount by \chimera@subfamily@col@yellow%
13256
+      \xdef\chimera@subfamily@col@green{\the\loopcount}%
13257
+      \loopcount=\chimera@subfamily@col@red\relax%
13258
+      \advance\loopcount by \chimera@subfamily@col@yellow%
13259
+      \xdef\chimera@subfamily@col@red{\the\loopcount}%
13260
+      \loopcount=\chimera@subfamily@col@blue\relax%
13261
+      \ifnum\chimera@subfamily@col@green>\loopcount\relax%
13262
+         \loopcount=\chimera@subfamily@col@green\relax%
13263
+      \else%
13264
+         \ifnum\chimera@subfamily@col@red>\loopcount\relax%
13265
+            \loopcount=\chimera@subfamily@col@red\relax%
13266
+         \fi%
13267
+      \fi%
13268
+      \xdef\max@green{\the\loopcount}%
13269
+      \loopcount=\chimera@subfamily@col@blue%
13270
+      \ifnum\max@green>0\relax%
13271
+         \multiply\loopcount by \max@yellow%
13272
+         \divide\loopcount by \max@green%
13273
+      \fi%
13274
+      \advance\loopcount by \chimera@subfamily@col@white%
13275
+      \multiply\loopcount by \temp@@%
13276
+      \divide\loopcount by \temp@count%
13277
+      \make@HEX%
13278
+      \xdef\nineth@{\seventh@}%
13279
+      \loopcount=\chimera@subfamily@col@green%
13280
+      \ifnum\max@green>0\relax%
13281
+         \multiply\loopcount by \max@yellow%
13282
+         \divide\loopcount by \max@green%
13283
+      \fi%
13284
+      \advance\loopcount by \chimera@subfamily@col@white%
13285
+      \multiply\loopcount by \temp@@%
13286
+      \divide\loopcount by \temp@count%
13287
+      \make@HEX%
13288
+      \xdef\nineth@{\seventh@\nineth@}%
13289
+      \loopcount=\chimera@subfamily@col@red%
13290
+      \ifnum\max@green>0\relax%
13291
+         \multiply\loopcount by \max@yellow%
13292
+         \divide\loopcount by \max@green%
13293
+      \fi%
13294
+      \advance\loopcount by \chimera@subfamily@col@white%
13295
+      \multiply\loopcount by \temp@@%
13296
+      \divide\loopcount by \temp@count%
13297
+      \make@HEX%
13298
+      \xdef\nineth@{\seventh@\nineth@}%
13299
+                     \ifx\chimera@labelOne@set\n@%
13300
+                        \xdef\chimera@labelOne@set{y}%
13301
+                        \xdef\chimera@label@subfamily{.\chimera@label@subfamily}%
13302
+                     \fi%
13303
+      \immediate\write\exp@rt@chimerafile{setattr a radius \temp@ \unexpanded{} #0:\chimera@res@num\chimerach@in @ca}%
13304
+      \immediate\write\exp@rt@chimerafile{setattr a color #\nineth@ \unexpanded{} #0:\chimera@res@num\chimerach@in @ca}%
13305
+      \immediate\write\exp@rt@chimerafile{setattr a name '|| \chimera@label@subfamily' #0:\chimera@res@num\chimerach@in @ca}%
13306
+      \ifshow@sublogo
13307
+         \ifnum\temp@@count>0 \else\temp@@count=1\fi%
13308
+         \loopcount=\temp@@count%
13309
+         \xdef\fourth@{\the\loopcount @}%
13310
+         \ifnum\loopcount>9999 \expandafter\decimal@A\fourth@ \else%
13311
+         \ifnum\loopcount>999  \expandafter\decimal@B\fourth@ \else%
13312
+         \ifnum\loopcount>99   \expandafter\decimal@C\fourth@ \else%
13313
+         \ifnum\loopcount>9    \expandafter\decimal@D\fourth@ \else%
13314
+                               \expandafter\decimal@E\fourth@%
13315
+         \fi\fi\fi\fi%
13316
+         \loopcount=-\chimera@remaining@col@red\relax%
13317
+         \xdef\chimera@remaining@col@red{\the\loopcount}%
13318
+         \loopcount=-\chimera@remaining@col@yellow\relax%
13319
+         \xdef\chimera@remaining@col@yellow{\the\loopcount}%
13320
+         \loopcount=-\chimera@remaining@col@blue\relax%
13321
+         \xdef\chimera@remaining@col@blue{\the\loopcount}%
13322
+         \loopcount=-\chimera@remaining@col@white\relax%
13323
+         \xdef\chimera@remaining@col@white{\the\loopcount}%
13324
+         \loopcount=-\chimera@remaining@col@black%
13325
+         \multiply\loopcount by 65535\relax%
13326
+         \divide\loopcount by \temp@count%
13327
+         \xdef\chimera@remaining@col@black{\the\loopcount}%
13328
+         \loopcount=65535\relax%
13329
+         \advance\loopcount by -\chimera@remaining@col@black%
13330
+         \xdef\temp@@{\the\loopcount}%
13331
+         \loopcount=\chimera@remaining@col@blue\relax%
13332
+         \ifnum\chimera@remaining@col@yellow>\loopcount\relax%
13333
+            \loopcount=\chimera@remaining@col@yellow\relax%
13334
+         \else%
13335
+            \ifnum\chimera@remaining@col@red>\loopcount\relax%
13336
+               \loopcount=\chimera@remaining@col@red\relax%
13337
+            \fi%
13338
+         \fi%
13339
+         \xdef\max@yellow{\the\loopcount}%
13340
+         \ifnum\chimera@remaining@col@blue<\chimera@remaining@col@yellow\relax%
13341
+            \xdef\chimera@remaining@col@green{\chimera@remaining@col@blue}%
13342
+         \else%
13343
+            \xdef\chimera@remaining@col@green{\chimera@remaining@col@yellow}%
13344
+         \fi%
13345
+         \loopcount=\chimera@remaining@col@yellow\relax%
13346
+         \advance\loopcount by -\chimera@remaining@col@green%
13347
+         \xdef\chimera@remaining@col@yellow{\the\loopcount}%
13348
+         \loopcount=\chimera@remaining@col@blue\relax%
13349
+         \advance\loopcount by -\chimera@remaining@col@green%
13350
+         \xdef\chimera@remaining@col@blue{\the\loopcount}%
13351
+         \ifnum\chimera@remaining@col@blue>0\relax%
13352
+            \ifnum\chimera@remaining@col@green>0\relax%
13353
+               \loopcount=\chimera@remaining@col@blue\relax%
13354
+               \multiply\loopcount by 2\relax \xdef\chimera@remaining@col@blue{\the\loopcount}%
13355
+               \loopcount=\chimera@remaining@col@green\relax%
13356
+               \multiply\loopcount by 2\relax \xdef\chimera@remaining@col@green{\the\loopcount}%
13357
+            \fi%
13358
+         \fi%
13359
+         \loopcount=\chimera@remaining@col@green\relax%
13360
+         \advance\loopcount by \chimera@remaining@col@yellow%
13361
+         \xdef\chimera@remaining@col@green{\the\loopcount}%
13362
+         \loopcount=\chimera@remaining@col@red\relax%
13363
+         \advance\loopcount by \chimera@remaining@col@yellow%
13364
+         \xdef\chimera@remaining@col@red{\the\loopcount}%
13365
+         \loopcount=\chimera@remaining@col@blue\relax%
13366
+         \ifnum\chimera@remaining@col@green>\loopcount\relax%
13367
+            \loopcount=\chimera@remaining@col@green\relax%
13368
+         \else%
13369
+            \ifnum\chimera@remaining@col@red>\loopcount\relax%
13370
+               \loopcount=\chimera@remaining@col@red\relax%
13371
+            \fi%
13372
+         \fi%
13373
+         \xdef\max@green{\the\loopcount}%
13374
+         \loopcount=\chimera@remaining@col@blue%
13375
+         \ifnum\max@green>0\relax%
13376
+            \multiply\loopcount by \max@yellow%
13377
+            \divide\loopcount by \max@green%
13378
+         \fi%
13379
+         \advance\loopcount by \chimera@remaining@col@white%
13380
+         \multiply\loopcount by \temp@@%
13381
+         \divide\loopcount by \temp@count%
13382
+         \make@HEX%
13383
+         \xdef\nineth@{\seventh@}%
13384
+         \loopcount=\chimera@remaining@col@green%
13385
+         \ifnum\max@green>0\relax%
13386
+            \multiply\loopcount by \max@yellow%
13387
+            \divide\loopcount by \max@green%
13388
+         \fi%
13389
+         \advance\loopcount by \chimera@remaining@col@white%
13390
+         \multiply\loopcount by \temp@@%
13391
+         \divide\loopcount by \temp@count%
13392
+         \make@HEX%
13393
+         \xdef\nineth@{\seventh@\nineth@}%
13394
+         \loopcount=\chimera@remaining@col@red%
13395
+         \ifnum\max@green>0\relax%
13396
+            \multiply\loopcount by \max@yellow%
13397
+            \divide\loopcount by \max@green%
13398
+         \fi%
13399
+         \advance\loopcount by \chimera@remaining@col@white%
13400
+         \multiply\loopcount by \temp@@%
13401
+         \divide\loopcount by \temp@count%
13402
+         \make@HEX%
13403
+         \xdef\nineth@{\seventh@\nineth@}%
13404
+                     \ifx\chimera@label@remainingOne@set\n@%
13405
+                        \xdef\chimera@label@remainingOne@set{y}%
13406
+                        \xdef\chimera@label@remaining{.\chimera@label@remaining}%
13407
+                     \fi%
13408
+         \immediate\write\exp@rt@chimerafile{setattr a radius \temp@ \unexpanded{} #1:\chimera@res@num\chimerach@in @ca}%
13409
+         \immediate\write\exp@rt@chimerafile{setattr a color #\nineth@ \unexpanded{} #1:\chimera@res@num\chimerach@in @ca}%
13410
+         \immediate\write\exp@rt@chimerafile{setattr a name '|| \chimera@label@remaining' #1:\chimera@res@num\chimerach@in @ca}%
13411
+      \fi%
13412
+}
13413
+\catcode`\"=12 \catcode`\#=6 \catcode`\~=13
13414
+\def\get@chimera@res@num#1,#2@{\xdef\chimera@res@num{#1}\xdef\chimera@stack{#2}}
13415
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
13416
+%%%%                     Chimera export routines   end                %%%%
13417
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
12734 13418
 \def\next@logo#1:#2,#3@{%
12735 13419
    \xdef\first@{#1}\xdef\second@{#2}\xdef\last@{#3}%
12736 13420
    \ifx\first@\ampers@nd%
13421
+      \ifx\exp@rt@chimera\y@%
13422
+        \xdef\chimera@stack{\chimera@stack @}%
13423
+        \expandafter\get@chimera@res@num\chimera@stack%
13424
+        \ifx\chimera@res@num\ampers@nd%
13425
+        \else%
13426
+            \write@chimera@data%
13427
+        \fi%
13428
+        \xdef\chimera@label@subfamily{}%
13429
+        \xdef\chimera@label@remaining{}%
13430
+        \xdef\chimera@subfamily@col@red{0}%
13431
+        \xdef\chimera@subfamily@col@blue{0}%
13432
+        \xdef\chimera@subfamily@col@yellow{0}%
13433
+        \xdef\chimera@subfamily@col@black{0}%
13434
+        \xdef\chimera@subfamily@col@white{0}%
13435
+        \xdef\chimera@remaining@col@red{0}%
13436
+        \xdef\chimera@remaining@col@blue{0}%
13437
+        \xdef\chimera@remaining@col@yellow{0}%
13438
+        \xdef\chimera@remaining@col@black{0}%
13439
+        \xdef\chimera@remaining@col@white{0}%
13440
+        \xdef\chimera@labelOne@set{n}%
13441
+        \xdef\chimera@labelTwo@set{n}%
13442
+        \xdef\chimera@labelThree@set{n}%
13443
+        \xdef\chimera@label@remainingOne@set{n}%
13444
+        \xdef\chimera@label@remainingTwo@set{n}%
13445
+        \xdef\chimera@label@remainingThree@set{n}%
13446
+      \fi%
12737 13447
      \ifx\clear@logo\n@%
12738 13448
      \ifx\hide@sig\n@%
12739 13449
       \expandafter\firstchar@get\sublogo@sig%
... ...
@@ -12755,12 +13465,10 @@
12755 13465
      \fi%
12756 13466
      \fi%
12757 13467
      \temp@count=0%
13468
+     \temp@@count=0%
12758 13469
      \kern\box@width%
12759 13470
      \advance\outerloopcount by 1 %
12760 13471
    \else%
12761
-    \ifnum#2=1%
12762
-      \temp@count=0%
12763
-    \else%
12764 13472
       \if\seq@type N%
12765 13473
          \loopcount=\second@%
12766 13474
          \multiply\loopcount by 2%
... ...
@@ -12796,7 +13504,7 @@
12796 13504
       \fi\fi\fi\fi%
12797 13505
       \xdef\third@{\fl@g\temp@}%
12798 13506
       \ifnum\temp@count<0 %
12799
-         \ifnum\second@<0 \else\temp@count=0 \fi%
13507
+         \ifnum\second@<0 \else\temp@@count=-\temp@count\relax\temp@count=0 \fi%
12800 13508
       \fi%
12801 13509
       \ifnum\temp@count>0 %
12802 13510
          \loopcount=\temp@count \xdef\fl@g{}%
... ...
@@ -12823,7 +13531,64 @@
12823 13531
          \kern-\box@width%
12824 13532
       \fi%
12825 13533
       \advance\temp@count by \second@%
12826
-    \fi%
13534
+      \xdef\temp@{\the\temp@count}%
13535
+      \ifx\exp@rt@chimera\y@%
13536
+         \xdef\temp@@{\csname chimera@col@\first@\endcsname}%
13537
+         \ifnum\second@<0 %
13538
+            \xdef\temp@@@{\csname chimera@remaining@col@\temp@@\endcsname}%
13539
+            \temp@count=\temp@@@%
13540
+            \advance\temp@count by \second@%
13541
+            \expandafter\xdef\csname chimera@remaining@col@\temp@@\endcsname{\the\temp@count}%
13542
+            \ifnum\second@<\label@threshold@lowerremainingIOOO%
13543
+                  \ifnum\second@<-999%
13544
+                     \ifx\chimera@label@remainingOne@set\n@%
13545
+                        \xdef\chimera@label@remainingOne@set{y}%
13546
+                        \xdef\chimera@label@remaining{.\chimera@label@remaining}%
13547
+                     \fi%
13548
+                  \fi%
13549
+                  \ifnum\second@<-1999%
13550
+                     \ifx\chimera@label@remainingTwo@set\n@%
13551
+                        \xdef\chimera@label@remainingTwo@set{y}%
13552
+                        \xdef\chimera@label@remaining{:\chimera@label@remaining}%
13553
+                     \fi%
13554
+                  \fi%
13555
+                  \ifnum\second@<-2999%
13556
+                     \ifx\chimera@label@remainingThree@set\n@%
13557
+                        \xdef\chimera@label@remainingThree@set{y}%
13558
+                        \xdef\chimera@label@remaining{>\chimera@label@remaining}%
13559
+                     \fi%
13560
+                  \fi%
13561
+                  \xdef\chimera@label@remaining{\first@\chimera@label@remaining}%
13562
+            \fi%
13563
+         \else%
13564
+            \xdef\temp@@@{\csname chimera@subfamily@col@\temp@@\endcsname}%
13565
+            \temp@count=\temp@@@%
13566
+            \advance\temp@count by \second@%
13567
+            \expandafter\xdef\csname chimera@subfamily@col@\temp@@\endcsname{\the\temp@count}%
13568
+            \ifnum\second@>\label@threshold@lowerIOOO%
13569
+                  \ifnum\second@>999%
13570
+                     \ifx\chimera@labelOne@set\n@%
13571
+                        \xdef\chimera@labelOne@set{y}%
13572
+                        \xdef\chimera@label@subfamily{.\chimera@label@subfamily}%
13573
+                     \fi%
13574
+                  \fi%
13575
+                  \ifnum\second@>1999%
13576
+                     \ifx\chimera@labelTwo@set\n@%
13577
+                        \xdef\chimera@labelTwo@set{y}%
13578
+                        \xdef\chimera@label@subfamily{:\chimera@label@subfamily}%
13579
+                     \fi%
13580
+                  \fi%
13581
+                  \ifnum\second@>2999%
13582
+                     \ifx\chimera@labelThree@set\n@%
13583
+                        \xdef\chimera@labelThree@set{y}%
13584
+                        \xdef\chimera@label@subfamily{>\chimera@label@subfamily}%
13585
+                     \fi%
13586
+                  \fi%
13587
+                  \xdef\chimera@label@subfamily{\first@\chimera@label@subfamily}%
13588
+            \fi%
13589
+         \fi%
13590
+      \fi%
13591
+      \temp@count=\temp@%
12827 13592
    \fi%
12828 13593
    \xdef\temp@{\last@.}%
12829 13594
    \ifx\temp@\d@t%
... ...
@@ -13125,10 +13890,23 @@
13125 13890
    \xdef\featureposttttop{1} \xdef\featureposbbbbottom{1}%
13126 13891
    \findc@nsensus%
13127 13892
    \noindent%
13893
+   \setlength{\bar@length}{0pt}%
13894
+   \xdef\fe@turep@s{top}%
13128 13895
    \ifnum\feature@ttttop=1
13896
+      \advance\bar@length by \feature@tttop\baselineskip%
13897
+      \advance\bar@length by \feature@ttop\baselineskip%
13898
+      \advance\bar@length by \feature@top\baselineskip%
13899
+      \multiply\bar@length by 2%
13900
+      \advance\bar@length by \tttt@sp@ce%
13901
+      \advance\bar@length by \ttt@sp@ce%
13902
+      \advance\bar@length by \tt@sp@ce%
13129 13903
       \ifnum\featureonttttop=0 \xdef\feature@ttttop{0} \fi
13130 13904
       \xdef\bottop@{ttttop}%
13905
+      \xdef\shift@feature{n}%
13131 13906
       \put@feature%
13907
+      \advance\bar@length by -\baselineskip%
13908
+      \ifx\shift@feature\y@ \vspace{-\bar@length}\fi%
13909
+      \setlength{\bar@length}{0pt}%
13132 13910
       \vspace{\tttt@sp@ce}%
13133 13911
       \vspace{-\baselineskip}%
13134 13912
       \newline\hbox{}%
... ...
@@ -13136,9 +13914,18 @@
13136 13914
       \iffix@\ifttttopfeature \vspace{\tttt@sp@ce}\newline\hbox{}\newline\hbox{}\fi\fi
13137 13915
    \fi
13138 13916
    \ifnum\feature@tttop=1
13917
+      \advance\bar@length by \feature@ttop\baselineskip%
13918
+      \advance\bar@length by \feature@top\baselineskip%
13919
+      \multiply\bar@length by 2%
13920
+      \advance\bar@length by \ttt@sp@ce%
13921
+      \advance\bar@length by \tt@sp@ce%
13139 13922
       \ifnum\featureontttop=0 \xdef\feature@tttop{0} \fi
13140 13923
       \xdef\bottop@{tttop}%
13924
+      \xdef\shift@feature{n}%
13141 13925
       \put@feature%
13926
+      \advance\bar@length by -\baselineskip%
13927
+      \ifx\shift@feature\y@ \vspace{-\bar@length}\fi%
13928
+      \setlength{\bar@length}{0pt}%
13142 13929
       \vspace{\ttt@sp@ce}%
13143 13930
       \vspace{-\baselineskip}%
13144 13931
       \newline\hbox{}%
... ...
@@ -13146,9 +13933,16 @@
13146 13933
       \iffix@\iftttopfeature \vspace{\ttt@sp@ce}\newline\hbox{}\newline\hbox{}\fi\fi
13147 13934
    \fi
13148 13935
    \ifnum\feature@ttop=1
13936
+      \advance\bar@length by \feature@top\baselineskip%
13937
+      \multiply\bar@length by 2%
13938
+      \advance\bar@length by \tt@sp@ce\message{tt\the\bar@length tt}%
13149 13939
       \ifnum\featureonttop=0 \xdef\feature@ttop{0} \fi
13150 13940
       \xdef\bottop@{ttop}%
13941
+      \xdef\shift@feature{n}%
13151 13942
       \put@feature%
13943
+      \advance\bar@length by -\baselineskip%
13944
+      \ifx\shift@feature\y@ \vspace{-\bar@length}\fi%
13945
+      \setlength{\bar@length}{0pt}%
13152 13946
       \vspace{\tt@sp@ce}%
13153 13947
       \vspace{-\baselineskip}%
13154 13948
       \newline\hbox{}%
... ...
@@ -13264,6 +14058,9 @@
13264 14058
          \ifnum\ruler@rot=0 \vspace{0.25\baselineskip}\fi%
13265 14059
       \fi%
13266 14060
    \fi%
14061
+   \xdef\fe@turep@s{bottom}%
14062
+   \setlength{\bar@length}{0pt}%
14063
+   \xdef\b@feature@count{0}
13267 14064
    \ifnum\feature@bottom=1 %
13268 14065
       \ifnum\featureonbottom=0 \xdef\feature@bottom{0}\fi%
13269 14066
       \xdef\bottop@{bottom}%
... ...
@@ -13273,6 +14070,9 @@
13273 14070
          \vspace{\b@r@stretch\box@height}%
13274 14071
       \fi%
13275 14072
       \put@feature%
14073
+      \temp@@count=\b@feature@count%
14074
+      \advance\temp@@count by 1%
14075
+      \xdef\b@feature@count{\the\temp@@count}%
13276 14076
    \else
13277 14077
       \iffix@
13278 14078
       \if\bottom@stretch y%
... ...
@@ -13285,14 +14085,24 @@
13285 14085
       \fi%
13286 14086
    \fi%
13287 14087
    \ifnum\feature@bbottom=1 %
14088
+      \advance\bar@length by \b@feature@count \baselineskip%
14089
+      \multiply\bar@length by \b@r@stretch%
14090
+      \multiply\bar@length by 2%
14091
+      \advance\bar@length by \bb@sp@ce\message{bb\the\bar@length bb}%
13288 14092
       \ifnum\featureonbbottom=0 \xdef\feature@bbottom{0}\fi%
13289 14093
       \xdef\bottop@{bbottom}%
13290 14094
       \vspace{\bb@sp@ce}%
13291 14095
       \if\bbottom@stretch y%
14096
+         \advance\bar@length by -\box@height%
14097
+         \advance\bar@length by \b@r@stretch\box@height%
13292 14098
          \vspace{-\box@height}%
13293 14099
          \vspace{\b@r@stretch\box@height}%
13294 14100
       \fi%
14101
+      \setlength{\bar@length}{0pt}%
13295 14102
       \put@feature%
14103
+      \temp@@count=\b@feature@count%
14104
+      \advance\temp@@count by 1%
14105
+      \xdef\b@feature@count{\the\temp@@count}%
13296 14106
    \else
13297 14107
       \iffix@
13298 14108
       \if\bbottom@stretch y%
... ...
@@ -13305,6 +14115,10 @@
13305 14115
       \fi
13306 14116
    \fi
13307 14117
    \ifnum\feature@bbbottom=1 %
14118
+      \advance\bar@length by \b@feature@count\baselineskip%
14119
+      \multiply\bar@length by \b@r@stretch%
14120
+      \multiply\bar@length by 2%
14121
+      \advance\bar@length by \bbb@sp@ce\message{bbb\the\bar@length bbb}%
13308 14122
       \ifnum\featureonbbbottom=0 \xdef\feature@bbbottom{0}\fi%
13309 14123
       \xdef\bottop@{bbbottom}%
13310 14124
       \vspace{\bbb@sp@ce}%
... ...
@@ -13313,6 +14127,9 @@
13313 14127
          \vspace{\b@r@stretch\box@height}%
13314 14128
       \fi%
13315 14129
       \put@feature%
14130
+      \temp@@count=\b@feature@count%
14131
+      \advance\temp@@count by 1%
14132
+      \xdef\b@feature@count{\the\temp@@count}%
13316 14133
    \else
13317 14134
       \iffix@
13318 14135
       \if\bbbottom@stretch y%
... ...
@@ -13325,6 +14142,10 @@
13325 14142
       \fi
13326 14143
    \fi
13327 14144
    \ifnum\feature@bbbbottom=1 %
14145
+      \advance\bar@length by \b@feature@count\baselineskip%
14146
+      \multiply\bar@length by \b@r@stretch%
14147
+      \multiply\bar@length by 2%
14148
+      \advance\bar@length by \bbbb@sp@ce\message{bbbb\the\bar@length bbbb}%
13328 14149
       \ifnum\featureonbbbbottom=0 \xdef\feature@bbbbottom{0}\fi%
13329 14150
       \xdef\bottop@{bbbbottom}%
13330 14151
       \vspace{\bbbb@sp@ce}%
... ...
@@ -14030,6 +14851,7 @@
14030 14851
     \fi
14031 14852
     \ifshow@sublogo \closein\sublogofile \fi
14032 14853
     \ifx\exp@rt\y@ \closeout\exp@rtfile \fi
14854
+    \ifx\exp@rt@chimera\y@ \closeout\exp@rt@chimerafile \fi%
14033 14855
     \closein\alignfile
14034 14856
     \message{)}
14035 14857
 }
... ...
@@ -14181,8 +15003,6 @@
14181 15003
     \ifnum\loopcount<\seq@count \repeat
14182 15004
     \xdef\seq@order{\seq@order,@}
14183 15005
  \killseq@count=\seq@count
14184
- \seq@percent=100
14185
- \ifnum\seq@count>0 \divide\seq@percent by \seq@count \fi
14186 15006
  \fi
14187 15007
  \fi
14188 15008
 }
... ...
@@ -14450,6 +15270,18 @@
14450 15270
            \caption[\c@pshort]{\c@p}
14451 15271
          \fi
14452 15272
       \fi
15273
+      \loopcount = \thresh@ld \multiply\loopcount by \seq@count \divide\loopcount by 100
15274
+      \xdef\thresh@ld@{\the\loopcount}
15275
+      \loopcount = \all@thresh@ld \multiply\loopcount by \seq@count \divide\loopcount by 100
15276
+      \xdef\all@thresh@ld@{\the\loopcount}
15277
+      \if\exp@rt@chimera\y@%
15278
+         \ifshow@logo%
15279
+             \init@chimera@file%
15280
+         \else%
15281
+         \ifshow@sublogo%
15282
+             \init@chimera@file%
15283
+         \fi\fi%
15284
+      \fi%
14453 15285
       \bgroup
14454 15286
          \ifx\out@put\y@\bigskip\fi
14455 15287
          \iffuncmode \show@consfalse \fi
... ...
@@ -14607,6 +15439,32 @@
14607 15439
 \expandafter\xdef\csname group@num1\endcsname{0}
14608 15440
 \expandafter\xdef\csname group@num2\endcsname{0}
14609 15441
 \xdef\exp@rt@num{0}       \xdef\exp@rt{n}
15442
+\xdef\exp@rt@chimera@num{1}   \xdef\exp@rt@chimera{n} \xdef\chimera@stack{}
15443
+\xdef\chimerab@llSc@le{1.0}
15444
+\memelabelcutoff{0.1}
15445
+\xdef\chimera@labelOne@set{n}
15446
+\xdef\chimera@labelTwo@set{n}
15447
+\xdef\chimera@labelThree@set{n}
15448
+\xdef\chimera@labelOne@remaining@set{n}
15449
+\xdef\chimera@labelTwo@remaining@set{n}
15450
+\xdef\chimera@labelThree@remaining@set{n}
15451
+\xdef\chimera@xdist@nce{0} \xdef\chimera@ydist@nce{40} \xdef\chimera@zdist@nce{0}
15452
+\xdef\chimerach@in{} \xdef\chimera@seqnum{0}
15453
+\xdef\chimera@label@subfamily{} \xdef\chimera@label@remaining{}
15454
+\memeStandardcolors
15455
+\xdef\chimera@subfamily@col@red{0}%
15456
+\xdef\chimera@subfamily@col@blue{0}%
15457
+\xdef\chimera@subfamily@col@yellow{0}%
15458
+\xdef\chimera@subfamily@col@black{0}%
15459
+\xdef\chimera@subfamily@col@white{0}%
15460
+\xdef\chimera@subfamily@col@none{0}%
15461
+\xdef\chimera@remaining@col@red{0}%
15462
+\xdef\chimera@remaining@col@blue{0}%
15463
+\xdef\chimera@remaining@col@yellow{0}%
15464
+\xdef\chimera@remaining@col@black{0}%
15465
+\xdef\chimera@remaining@col@white{0}%
15466
+\xdef\chimera@remaining@col@none{0}%
15467
+\xdef\echo@filename{}
14610 15468
 \xdef\divref@{0}
14611 15469
 \xdef\all@thresh@ld{100}  \all@shadefalse
14612 15470
 \hidefeaturenames         \hidefeaturestylenames