Hi<br> I would like to add to what Mr.Shameer has said.<br> When DNA is a ligand, in many PDB files, it goes with ATOM instead of HETATM -token; in such cases<br> you can "grep" on "A or T or C or G" for residue-name field.
<br><br>Regards<br>Kalidas. Y<br><br><div><span class="gmail_quote">On 10/20/06, <b class="gmail_sendername">Shameer Khadar</b> <<a href="mailto:skhadar@gmail.com">skhadar@gmail.com</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<span class="gmail_quote"></span>I strongly beleive this can be done using a 'grep' and 'substitution' commands in linux. <br>Since the ligand data starts with HETATM, they can be easily grepable. <br><br>No need any 'parser' - a simple perl script can do this !
<br>Cheers, <br><span>Shameer Khadar<br>NCBS-TIFR <br>B'lore </span><div><span><br> <br><div><span class="gmail_quote">On 10/20/06, <b class="gmail_sendername">Tomek Jarzynka
</b> <<a href="mailto:tomee@genesilico.pl" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">tomee@genesilico.pl</a>> wrote:
</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi,<br><br>I would like to create a script that would take a PDB file as input,<br>try and identify the ligand structures and delete them from the PDB
<br>file. I figured this would be possible with Biopython by looking at<br>the atom id (whether it contains 'H_') and subclassing Select to<br>not allow those items to be written to a file.<br>Is there any more elegant way of doing this, perhaps another PDB parser
<br>framework, or maybe someone has already done similar work?<br><br>Thanks in advance,<br>--<br>Tomasz K. Jarzynka / +48 601 706 601 / tomee(a-t)genesilico(d-o-t)pl<br>Laboratory of Bioinformatics and Protein Engineering |
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<br><br></blockquote></div><br><br clear="all"><br>-- <br>Kalidas Y<br><a href="http://ssl.serc.iisc.ernet.in/~kalidas">http://ssl.serc.iisc.ernet.in/~kalidas</a>