<html><body><div style="color:#000; background-color:#fff; font-family:HelveticaNeue-Light, Helvetica Neue Light, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:16px"><div><br></div><div dir="ltr">Hi Joao,</div><div id="yui_3_16_0_1_1414338837971_7802" dir="ltr">Thank you for response.</div><div id="yui_3_16_0_1_1414338837971_7450" dir="ltr">If all residues aren't resolved in crystal, then extracting sequence from pdb, wouldn't be a good call.</div><div id="yui_3_16_0_1_1414338837971_7803" dir="ltr"><br> </div><div id="yui_3_16_0_1_1414338837971_7449" class="qtdSeparateBR"><div id="yui_3_16_0_1_1414338837971_7453" dir="ltr">I will be working a lot [~100s or 1000s] in near future. Is there any way, I can find break in my pdb file?<br></div><div id="yui_3_16_0_1_1414338837971_7804" dir="ltr"><br></div><div dir="ltr">- Another doubt, I've, while printing the chain.ids in script. Many times, I get chain " ", that is a space. </div><div id="yui_3_16_0_1_1414338837971_7853" dir="ltr">In script sent, code looks like:</div><div dir="ltr"><br></div><div id="yui_3_16_0_1_1414338837971_7857" dir="ltr"> st=PDBParser(QUIET=True).get_structure('X',i)<br style="" class=""> ko=st.get_chains()<br style="" class=""> for i in ko:<br style="" class=""> print i.id </div><div id="yui_3_16_0_1_1414338837971_7858" dir="ltr"><br></div><div id="yui_3_16_0_1_1414338837971_7859" dir="ltr">Why space name is present? <br></div><div id="yui_3_16_0_1_1414338837971_7860" dir="ltr"><br></div><div id="yui_3_16_0_1_1414338837971_7805" dir="ltr">Thanks.<br></div><br></div><div id="yui_3_16_0_1_1414338837971_7435" style="display: block;" class="yahoo_quoted"> <div id="yui_3_16_0_1_1414338837971_7434" style="font-family: HelveticaNeue-Light, Helvetica Neue Light, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 16px;"> <div id="yui_3_16_0_1_1414338837971_7433" style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 16px;"> <div id="yui_3_16_0_1_1414338837971_7447" dir="ltr"> <font id="yui_3_16_0_1_1414338837971_7448" face="Arial" size="2"> On Saturday, October 25, 2014 12:32 AM, João Rodrigues <anaryin@gmail.com> wrote:<br> </font> </div> <br><br> <div id="yui_3_16_0_1_1414338837971_7432" class="y_msg_container"><div id="yiv1026798545"><div id="yui_3_16_0_1_1414338837971_7431"><div id="yui_3_16_0_1_1414338837971_7430" dir="ltr">Hi there,<div id="yui_3_16_0_1_1414338837971_7436"><br clear="none"></div><div id="yui_3_16_0_1_1414338837971_7429">The numbering in your PDB file is not continuous and it matches to regions in the structure that are missing residues. Open your PDB structure in Pymol and you'll see. Alternatively, print the C-N distances (peptide bond) for consecutive residues and you'll also notice when they are larger than ~3Å it corresponds to your break. <br clear="none"></div><div><br clear="none"></div><div id="yui_3_16_0_1_1414338837971_7446">As for your discrepancy between the sequences in the FASTA file and the PDB, that's just because not all residues are resolved in the crystal structure.</div><div><br clear="none"></div><div>Cheers,</div><div><br clear="none"></div><div>João</div></div><div class="yiv1026798545gmail_extra"><br clear="none"><div class="yiv1026798545gmail_quote">2014-10-24 13:10 GMT-05:00 Sanjeev Sariya <span dir="ltr"><<a rel="nofollow" shape="rect" ymailto="mailto:s.sariya_work@ymail.com" target="_blank" href="mailto:s.sariya_work@ymail.com">s.sariya_work@ymail.com</a>></span>:<br clear="none"><blockquote class="yiv1026798545gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div class="yiv1026798545yqt2833603735" id="yiv1026798545yqt94098"><div><div style="color:#000;background-color:#fff;font-family:HelveticaNeue-Light, Helvetica Neue Light, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:16px;"><div dir="ltr">Hi All,</div><div dir="ltr">I'm having a hard time using and understanding biopython pdb.</div><div dir="ltr">./read_pdb_file.py 3OE6.pdb</div><div dir="ltr"><br clear="none"></div><div dir="ltr">I'm attaching python script, pdb file, fasta file and output with mail.</div><div dir="ltr">I'have following doubts:</div><div dir="ltr">- When I print the sequence I get in broken pieces. Why?</div><div dir="ltr">- Also the sequence printed doesn't match with the fasta file (attached).</div><div dir="ltr">- Am I doing making a silly mistake?</div><div dir="ltr"><br clear="none"></div><div dir="ltr">I am running script as:<br clear="none"></div><div dir="ltr">python read_pdb_file.py 3OE6.pdb </div><div dir="ltr"><br clear="none"></div><div dir="ltr">Kindly help and guide.<br clear="none"></div><div dir="ltr"><br clear="none"></div></div></div></div><br clear="none">_______________________________________________<br clear="none">
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