<div dir="ltr">Ola Claudia,<div><br></div><div>You don't need to instantiate PDBParser at every structure. Once is enough followed by calling get_structure() for each structure.</div><div><br></div><div>As for the merging, the problem is that set_structure sets one structure only. What you want is to actually start with an "empty" structure/model object (you have to create them yourself) and then just append the chains from your structures to it. If they have different chain identifiers, there should be no conflict and it should be straightforward.</div>
<div><br></div><div>Does this make sense?</div><div><br></div><div>Best,</div><div><br></div><div>João</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">2014-06-25 17:48 GMT+02:00 Claudia Millán Nebot <span dir="ltr"><<a href="mailto:cmncri@ibmb.csic.es" target="_blank">cmncri@ibmb.csic.es</a>></span>:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi :) I'm newbie to BioPython and I am trying to do the following:<div><br></div><div>I have a set of different pdbs that I want to merge together into a single file. I would like to take into consideration that there could be issues with the naming, so, after reading a few other posts in this same list, I came up with the following code:</div>
<div><br></div><div><div> list_parsers=[]</div><div> list_of_structures=[]</div><div> for index in range(len(list_of_filenames)):</div><div> parser=PDBParser()</div><div> list_parsers.append(parser)</div>
<div> structure=parser.get_structure(list_of_filenames[index][:-4],list_of_filenames[index])</div><div> list_of_structures.append(structure)</div><div> i_chain = 65</div><div> for structure in list_of_structures:</div>
<div> for chain in structure:</div><div> <a href="http://chain.id" target="_blank">chain.id</a> = chr(i_chain)</div><div> i_chain += 1</div><div> io=PDBIO() </div>
<div> for structure in list_of_structures:</div>
<div> io.set_structure(structure)</div><div> io.save(clust_fold+key[:-4]+"_fused.pda")</div><div><br></div><div>This is not working, as I guess i'm just changing the structure set each time I do io.set_structure, and writing the last one. And as there is not such a thing as the append_structure() method I have just tried a silly thing. So my question would be which is the best way to get the pdbs merged? Should I save as independent unfold entities and then write them by using a Select class?</div>
<div><br></div><div>Thanks in advance and regards,</div><div><div><div dir="ltr"><span style="font-family:arial,sans-serif;font-size:13px;border-collapse:collapse;color:rgb(34,34,34)"><p><font face="arial, helvetica, sans-serif">Claudia Millán (<a href="mailto:cmncri@ibmb.csic.es" style="color:rgb(17,85,204)" target="_blank">cmncri@ibmb.csic.es</a>)</font></p>
<p><font face="arial, helvetica, sans-serif">Crystallographic Methods Group</font></p><p><font face="arial, helvetica, sans-serif"> <a href="http://chango.ibmb.csic.es" target="_blank">http://chango.ibmb.csic.es</a> <br>
</font></p>
<p><font face="arial, helvetica, sans-serif">Institut de Biologia Molecular de Barcelona (IBMB-CSIC)</font></p><p><font face="arial, helvetica, sans-serif">Barcelona, Spain</font></p></span></div></div>
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