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#!perl

...
                   A 172    HIS       A  95    HIS^?     
                   A 267    ASP       A  98    ASP~?

$ multiline_join.pl
line=ULMNm  3  1fdy_07      N-ACETYLNEURAMINATE LYASE           user  
+ 1           3                                      RMSD =     1.06 A
+  MATRIX:   -0.3862 -0.2080 -0.8987  0.6457  0.6347 -0.4244 -0.6587  
+0.7442  0.1108   -16.917   -91.429   -35.632                     D  4
+7    SER       A  57    SER.?                        D  48    THR    
+   A  56    THR.?                        D 165    LYS       A  33    
+LYS~?      
line=ULMNm  3  2tmd_00      TRIMETHYLAMINE DEHYDROGENASE        user  
+ 1           3                                      RMSD =     1.15 A
+  MATRIX:    0.9011 -0.4313  0.0445 -0.1032 -0.3130 -0.9441 -0.4211 -
+0.8462  0.3266    52.913    23.262    25.449                     A 16
+9    TYR       A  41    TYR~?                        A 172    HIS    
+   A  95    HIS^?                        A 267    ASP       A  98    
+ASP~?