<div>Ah! That you can disable with write_end=False to PDBIO save().<div><br></div>
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<br><br><div class="gmail_quote"><p>On Tue, Oct 27, 2015 at 4:39 PM, Claudia Millán Nebot <span dir="ltr"><<a href="mailto:cmncri@ibmb.csic.es" target="_blank">cmncri@ibmb.csic.es</a>></span> wrote:<br></p><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div>
<div dir="ltr">Sorry, I meant the END statement :)</div>
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<br><div class="gmail_quote">2015-10-27 16:37 GMT+00:00 João Rodrigues <span dir="ltr"><<a href="mailto:j.p.g.l.m.rodrigues@gmail.com">j.p.g.l.m.rodrigues@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<span><div>Hi Claudia,</div>
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<div>The TER statement *should* show up at the end of each chain, so it’s OK.</div>
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<div>Best,</div>
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<div>João</div></span><div class="HOEnZb"><div class="h5">
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<p>On Tue, Oct 27, 2015 at 3:40 PM, Claudia Millán Nebot <span dir="ltr"><<a href="mailto:cmncri@ibmb.csic.es">cmncri@ibmb.csic.es</a>></span> wrote:<br></p>
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<div dir="ltr">Dear Hongbo and <span style="font-size:13px;white-space:nowrap">João,</span><div>
<span style="white-space:nowrap"><br></span><div>thank you both! I got my models named right now, but as <span style="font-size:13px;white-space:nowrap">João points out, the TER keeps appearing. </span>
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<span style="font-size:13px;white-space:nowrap">Anyway, I am happy that it is something that can be </span><span style="white-space:nowrap">helpful for other cases </span><span style="white-space:nowrap">because it is a general problem in the writing of</span>
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<div><span style="white-space:nowrap">the file. I will updgrade my Biopython installation as soon as the fix is available. Thanks again! :)</span></div>
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<div><span style="white-space:nowrap">Best,</span></div>
<div><span style="white-space:nowrap"><br></span></div>
<div><span style="white-space:nowrap">Claudia</span></div>
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<br><div class="gmail_quote">2015-10-27 13:40 GMT+00:00 Hongbo Zhu 朱宏博 <span dir="ltr"><<a href="mailto:macrozhu@gmail.com">macrozhu@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">if you look at PDBIO.py :<div><br></div>
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<div><font face="monospace, monospace">if model_flag:</font></div>
<div><font face="monospace, monospace"> fp.write("MODEL %s\n" % model.serial_num)</font></div>
</div><div>so model.serial_num is written, not <a href="http://model.id">model.id</a>. </div>
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<div>Although the BioPython FAQ says:</div>
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<h4 style="color:rgb(0,0,0);margin:0px 0px 0.3em;overflow:hidden;padding-top:0.5em;padding-bottom:0.17em;border-bottom-style:none;width:auto;font-size:14.848px;font-family:sans-serif;line-height:19.2px;background-image:none;background-repeat:initial"><span>What is a model id?</span></h4>
<p style="margin:0.4em 0px 0.5em;line-height:19.2px;color:rgb(0,0,0);font-family:sans-serif;font-size:12.8px">The model id is an integer which denotes the rank of the model in the PDB/mmCIF file. The model is starts at 0. Crystal structures generally have only one model (with id 0), while NMR files usually have several models.</p>
<p style="margin:0.4em 0px 0.5em;line-height:19.2px;color:rgb(0,0,0);font-family:sans-serif;font-size:12.8px"><br></p>
<p style="margin:0.4em 0px 0.5em;line-height:19.2px;color:rgb(0,0,0);font-family:sans-serif;font-size:12.8px">So perhaps one of them should be updated?</p>
<span><font color="#888888"><p style="margin:0.4em 0px 0.5em;line-height:19.2px;color:rgb(0,0,0);font-family:sans-serif;font-size:12.8px">hongbo</p></font></span>
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