Am I missing something when I interpret OP's spec, "I'd like to store everything starting from 'line=ULMNm' till before the next 'line=ULMNm' as one string", as meaning the sample data should be divided into elements, each with a single element begining with "line=" and ending with the first instance of two newlines?

Missing something or not, that's how I read it in writing this to satisfy my understanding of the spec:

#!/usr/bin/perl
use strict;
use warnings;
# 864768

my @words = split /(line=)/, do { local $/="\n\n"; <DATA> };     # a v
+ariant of moritz' advice

for my $words(@words) {
        chomp $words;
        if ($words eq "line=") {
            print $words;    
        }else{
            print "$words \n -------\n";  # the dashes visually separa
+te the output records
        }
}

exit;

__DATA__ 
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  47    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 169    TYR       A  41    TYR~?     
                   A 172    HIS       A  95    HIS^?     
                   A 267    ASP       A  98    ASP~?     
 
line=ULMNm  3  4fdy_07      P-HYDROOXIDE           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  47    SER       A  57    SER.?     
                   D  48    THR       A  56    THR.?     
                   D 165    PQR       A  33    PRQ~?     
 
line=ULMNm  3  5tmd_00      BAZ    Blivitz        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 169    TYR       A  41    TYR~?     
                   A 172    HIS       A  95    HIS^?     
                   A 267    XYZ       A  98    XYZ~?

[download]

and we see this, upon execution:

F:\_wo\pl_test>perl 864768.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  47    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 169    TYR       A  41    TYR~?
                   A 172    HIS       A  95    HIS^?
                   A 267    ASP       A  98    ASP~?

 -------
line=ULMNm  3  4fdy_07      P-HYDROOXIDE           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  47    SER       A  57    SER.?
                   D  48    THR       A  56    THR.?
                   D 165    PQR       A  33    PRQ~?

 -------
line=ULMNm  3  5tmd_00      BAZ Blivitz        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 169    TYR       A  41    TYR~?
                   A 172    HIS       A  95    HIS^?
                   A 267    XYZ       A  98    XYZ~?
 -------

F:\_wo\pl_test>

[download]

Note the empty record that is the first output. Not good... hence, I'd welcome comments on my algorithm/code AND any comments rebutting my interpretation of the spec.

Belated addition, 2125 EDT (U.S., roughly 10 hours later): Re OP's question about storing the munged data in variables. Whilst working this out, I used Data::Dumper to try to ascertain why an earlier iteration didn't work... and after fixing my foolishness but before removing D::D from the code, observed that D::D's list of vars had "line=" (see split at line 10) in Var2, Var4... and the rest of each munged data section in Var3, Var5, ....

In reply to Re: regex question: store multiple lines as a string by ww
in thread regex question: store multiple lines as a string by nurulnad

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.