<div dir="ltr"><div><div>Hi, João, <br><br></div>AFAIK, "fit" means "superimpose", rather than "align" in PyMOL. That is, the proteins have to be same, like different models in a NMR structure. It is unclear if Patrick's proteins are so. Since he mentioned "align", I just presume he has different proteins.<br></div><div>In addition, PyMOL is quite picky if you ask it to (be) fit :-)<br><a href="http://www.pymolwiki.org/index.php/Rms">http://www.pymolwiki.org/index.php/Rms</a><br></div><div><br></div><div>Yes it is getting off topic. I guess Patrick needs to provide more info if he needs more help. <br></div><div>cheers,<br></div><div>hongbo<br></div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Feb 25, 2015 at 5:03 PM, João Rodrigues <span dir="ltr"><<a href="mailto:j.p.g.l.m.rodrigues@gmail.com" target="_blank">j.p.g.l.m.rodrigues@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><p dir="ltr">Hi Hongbo, </p>
<p dir="ltr">Slightly off-topic but.. In Pymol you can use intra_fit to align models of an ensemble and view the multiple states without splitting. </p>
<p dir="ltr">Cheers, </p>
<p dir="ltr">João </p>
<br><div class="gmail_quote">A qua, 25/02/2015, 16:48, Hongbo Zhu 朱宏博 <<a href="mailto:macrozhu@gmail.com" target="_blank">macrozhu@gmail.com</a>> escreveu:<div><div class="h5"><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div>Hi, Patrick, <br><br></div>if you just want to visualized the aligned structures, you can load them one by one in PyMOL. Merging them as different models in one PDB is not necessary. Perhaps it is even not optimal: you have to "split" the models in PyMOL if you want to view them all.<br></div>You can open multiple PDB files in the same directory using PyMOL by typing:<br></div><span style="font-family:monospace,monospace">pymol *.pdb</span><br><div class="gmail_extra"><br></div><div class="gmail_extra">You can also align structures within PyMOL. Several methods are available:<br><a href="http://www.pymolwiki.org/index.php/Align" target="_blank">http://www.pymolwiki.org/index.php/Align</a><br><br></div><div class="gmail_extra">cheers,<br></div><div class="gmail_extra">hongbo<br></div><div class="gmail_extra"></div></div><div dir="ltr"><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Feb 24, 2015 at 11:45 PM, PC <span dir="ltr"><<a href="mailto:patrick.cossins@inbox.com" target="_blank">patrick.cossins@inbox.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi,<br>
<br>
I have the following PDB's<br>
<br>
A.pdb<br>
B.pdb<br>
C.pdb<br>
D.pdb<br>
<br>
I can align B, C , D with A but I want to write ALL four structures in one file to open in a views like pymol.<br>
<br>
io = Bio.PDB.PDBIO()<br>
io.set_structure(moving_structure)<br>
io.save("moved.pdb")<br>
<br>
This has one file, on the second iteration I want to append to moved.pdb the other pdb's.<br>
How can I do that in biopython?<br>
<br>
Thank you,<br>
Patrick<br>
<br>
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</blockquote></div><br><br clear="all"><br></div></div><div dir="ltr"><div class="gmail_extra">-- <br><div>Hongbo</div>
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