Mark

Thanks for your reply, I apologise for not explaining further. $ref is simply the atom number in the PDB file, which is a unique number for every atom.

Hence, your solution would work just as well, as every line has in itself, the chain id and residue details

However, PDB files can be large, for example, the one Im dealing with right now has 30 models, of two chains with thousands of atoms, so thats 50k $ref to step through, and in many case, Im just stepping through the models, chains, or residues.

Being able to choose one chain directly would half the number of atoms to step through.

Any more suggestions?

Thanks
Sam Seaver

In reply to Re: Re: Optimizing PDB data structures by seaver
in thread Optimizing PDB data structures by seaver

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.